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		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2688391</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2688391"/>
		<updated>2016-12-05T15:54:20Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region via genetic engineering&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on a cell are neutralized when bound to high affinity receptor binding sites on the drug&amp;lt;ref name=&amp;quot;wong&amp;quot;&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/2&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/6&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α is a cytokine secreted by macrophages to elicit an inflammatory resopnse. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref name=&amp;quot;wong&amp;quot;/&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor of TNF-R. If an adequate amount of Remicade, or other competitive inhibitor, is introduced the TNF-α binding interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/2&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref name=&amp;quot;grainger&amp;quot;&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref name=&amp;quot;grainger&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref name=&amp;quot;kircik&amp;quot;&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2688390</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2688390"/>
		<updated>2016-12-05T15:42:56Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region via genetic engineering&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on a cell are neutralized when bound to high affinity receptor binding sites on the drug&amp;lt;ref name=&amp;quot;wong&amp;quot;&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/2&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/6&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α is a cytokine secreted by macrophages to elicit an inflammatory resopnse. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref name=&amp;quot;wong&amp;quot;/&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor of TNF-R. If an adequate amount of Remicade, or other competitive inhibitor, is introduced the TNF-α binding interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref name=&amp;quot;grainger&amp;quot;&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref name=&amp;quot;grainger&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref name=&amp;quot;kircik&amp;quot;&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_99999&amp;diff=2688037</id>
		<title>Sandbox 99999</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_99999&amp;diff=2688037"/>
		<updated>2016-11-30T23:39:53Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: New page: ==Your Heading Here (maybe something like &amp;#039;Structure&amp;#039;)== 0 &amp;lt;StructureSection load=&amp;#039;1stp&amp;#039; size=&amp;#039;340&amp;#039; side=&amp;#039;right&amp;#039; caption=&amp;#039;Caption for this structure&amp;#039; scene=&amp;#039;&amp;#039;&amp;gt; This is a default text for y...&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Your Heading Here (maybe something like &#039;Structure&#039;)== 0&lt;br /&gt;
&amp;lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Sandbox 99999&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Test ==&lt;br /&gt;
Starch metabolism is a key process in plants and other organisms. It is an important in the storage of starch and utilization for other processes in the living cycles of plants. Starch is a stored carbohy-drate in plants which can later be used in carbohy-drate metabolism which plays an essential role in generating energy for the plant when there isn’t light available. Rather, starch is stored up until the night time when light isn’t available and continues creating energy for itself when photosynthesis cannot be done.&lt;br /&gt;
There are several enzymes associated with starch metabolism, the focus will be β-amylase (BAM) in the regulation process. β-amylase has an important role in degradation of starches within the plant. This study will focus on Arabidopsis tha-liana and the Arabidopsis plants generally have nine genes encoding for different types of β-amylases. Of the nine types, there is little infor-mation available for BAM6 or 7. While several of the BAM have confirmed catalytic activity within the plant, there is not enough data available for activity of BAM6 and 7, so structural analysis of both enzymes will be conducted using bioinformat-ics programs in order to predict functional similar-ities to other known BAM proteins. &lt;br /&gt;
Another featured studied with BAM proteins are the post-translational regulators of certain BAM types. Different post-translational regulators can change a variety of features of the protein, inhibi-tion, or protein interaction and more. The study will focus on glutathione (GSH), which is partly known to have some post-translational modifica-tions on a few of the known BAM proteins. The analysis of GSH modification of both BAM6 and BAM7 will be tested. &lt;br /&gt;
The structural similarities of BAM6 and BAM7 will be compared to each other as well as known BAM proteins in order to predict active or inactive functionality of the protein. The following proce-dures will follow a series of tests to determine the post-translational modifications of GSH on BAM. To validate the computational program experiments on BAM6 and 7, they will be followed up by an x-ray crystallography and Förster resonance energy transfer experiment to validate findings from the relevant computational data.&lt;br /&gt;
JPRED4&lt;br /&gt;
To determine the secondary structure of the pro-tein sequence of BAM6 and BAM7, JPRED4 was utilized. The webserver requires a single protein sequence and uses known homologs to output sec-ondary structure information on the sequence. The program utilizes an algorithm called Jnet to make secondary structure predictions of 82% or greater accuracy. JPRED4 will provide basic knowledge on the functional regions of both BAM proteins. &lt;br /&gt;
SwissModel&lt;br /&gt;
&lt;br /&gt;
Enzyme that is part of starch breakdown - regu-lator&lt;br /&gt;
Sequence for Arabidopsis thaliana (β-AM-6 and BAM-7), however is found in many species includ-ing humans&lt;br /&gt;
β-AM has ~9 different forms in Ara. Some forms are active, some are inactive&lt;br /&gt;
Starch Metabolic pathways, starch is the most common carbohydrate found in plants. β-AM a part of starch degradation pathway in Ara (essential). &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2687702</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2687702"/>
		<updated>2016-11-17T14:33:36Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on a cell are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref name=&amp;quot;wong&amp;quot;&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/2&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref name=&amp;quot;wong&amp;quot;/&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref name=&amp;quot;grainger&amp;quot;&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref name=&amp;quot;grainger&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref name=&amp;quot;kircik&amp;quot;&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686773</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686773"/>
		<updated>2016-11-08T19:44:10Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref name=&amp;quot;wong&amp;quot;&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/2&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref name=&amp;quot;wong&amp;quot;/&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref name=&amp;quot;grainger&amp;quot;&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref name=&amp;quot;grainger&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref name=&amp;quot;kircik&amp;quot;&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686772</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686772"/>
		<updated>2016-11-08T19:41:56Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref name=&amp;quot;wong&amp;quot;&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/2&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref name=&amp;quot;wong&amp;quot;/&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref name=&amp;quot;grainger&amp;quot;&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref name=&amp;quot;grainger&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref name=&amp;quot;kircik&amp;quot;&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686771</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686771"/>
		<updated>2016-11-08T18:57:31Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref name=&amp;quot;wong&amp;quot;&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref name=&amp;quot;wong&amp;quot;/&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref name=&amp;quot;grainger&amp;quot;&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref name=&amp;quot;grainger&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref name=&amp;quot;kircik&amp;quot;&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref name=&amp;quot;kircik&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686770</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686770"/>
		<updated>2016-11-08T18:25:43Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref name=&amp;quot;liang&amp;quot;&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;liang&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686769</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686769"/>
		<updated>2016-11-08T14:32:27Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686735</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686735"/>
		<updated>2016-11-07T21:53:39Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites&amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR)&amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines&amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686734</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686734"/>
		<updated>2016-11-07T21:50:50Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites&amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR)&amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines&amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;&amp;lt;/ref&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;&amp;lt;/ref&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies&amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686725</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686725"/>
		<updated>2016-11-07T16:36:12Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process&amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites&amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt;&amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR)&amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines&amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer&amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686724</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686724"/>
		<updated>2016-11-07T16:29:20Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686723</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686723"/>
		<updated>2016-11-07T15:59:31Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a &amp;lt;scene name=&#039;74/744162/Hydrophobic_interface/1&#039;&amp;gt;hydrophobic interface&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686720</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686720"/>
		<updated>2016-11-07T14:38:15Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/3&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface &amp;lt;ref&amp;gt;PMID:2777790&amp;lt;/ref&amp;gt; through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues &amp;lt;scene name=&#039;74/744162/Cdef_residues/1&#039;&amp;gt;Gln67–His73 and Gln102–Lys112&amp;lt;/scene&amp;gt; of the C-D and E-F loops &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686679</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686679"/>
		<updated>2016-11-03T15:10:31Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;4g3y, Biological Assembly 1, Resolution 2.6Å&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt;PMID:17592358&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors (TNF-R?) on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. To view the loop residues of the full structure complex, &amp;lt;scene name=&#039;74/744162/Loops_tnf_3molecule/1&#039;&amp;gt;click here&amp;lt;/scene&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt;PMID:17916444&amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt;PMID:27100432&amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt;PMID:23504311&amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt;REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt;Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt;PMID:19537380&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686678</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2686678"/>
		<updated>2016-11-03T13:46:50Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt; PMID: 17592358 &amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/2&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt; PMID: 27100432 &amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685963</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685963"/>
		<updated>2016-11-02T16:30:56Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt; PMID: 17592358 &amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. &amp;lt;scene name=&#039;74/744162/Heavy_chain/1&#039;&amp;gt;The heavy chain region is highlighted here, and only (1 of 3) molecules are shown, for simplicity&amp;lt;/scene&amp;gt;. In addition, the &amp;lt;scene name=&#039;74/744162/Light_chain/1&#039;&amp;gt;light chain&amp;lt;/scene&amp;gt; is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt; PMID: 27100432 &amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685327</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685327"/>
		<updated>2016-11-01T14:23:19Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt; PMID: 17592358 &amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor &amp;lt;ref name=&amp;quot;businessIn&amp;quot;/&amp;gt;. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt; PMID: 27100432 &amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685326</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685326"/>
		<updated>2016-11-01T14:18:18Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt; PMID: 17592358 &amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt; PMID: 27100432 &amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685324</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685324"/>
		<updated>2016-11-01T14:15:10Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref&amp;gt; PMID: 17592358 &amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt; &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) &amp;lt;ref&amp;gt; PMID: 17916444 &amp;lt;/ref&amp;gt;. Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines &amp;lt;ref&amp;gt; PMID: 27100432 &amp;lt;/ref&amp;gt;. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region of TNF. This arises when TNF-α is in its active form and exists as a trimer &amp;lt;ref&amp;gt; PMID: 23504311 &amp;lt;/ref&amp;gt;. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685322</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685322"/>
		<updated>2016-11-01T13:44:17Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref name=&amp;quot;JBC1&amp;quot;&amp;gt;Shuaiyi Liang Jianxin Dai Sheng Hou Lishu Su Dapeng Zhang Huaizu Guo Shi Hu Hao Wang Zihe Rao Yajun Guo Zhiyong Lou. (2013). Structural basis for treating tumor necrosis factor α (TNFα)-associated diseases with the therapeutic antibody infliximab. Journal of Biologocal Chemistry, 288, 13799. DOI:10.1074/jbc.M112.433961&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685318</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685318"/>
		<updated>2016-11-01T13:34:08Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref name=&amp;quot;JBC1&amp;quot;&amp;gt;Shuaiyi Liang Jianxin Dai Sheng Hou Lishu Su Dapeng Zhang Huaizu Guo Shi Hu Hao Wang Zihe Rao Yajun Guo Zhiyong Lou. (2013). Structural basis for treating tumor necrosis factor α (TNFα)-associated diseases with the therapeutic antibody infliximab. Journal of Biologocal Chemistry, 288, 13799. DOI:10.1074/jbc.M112.433961&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops [[Image:Example.jpg]]. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685317</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2685317"/>
		<updated>2016-11-01T12:04:31Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (Infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process &amp;lt;ref name=&amp;quot;JBC1&amp;quot;&amp;gt;Shuaiyi Liang Jianxin Dai Sheng Hou Lishu Su Dapeng Zhang Huaizu Guo Shi Hu Hao Wang Zihe Rao Yajun Guo Zhiyong Lou. (2013). Structural basis for treating tumor necrosis factor α (TNFα)-associated diseases with the therapeutic antibody infliximab. Journal of Biologocal Chemistry, 288, 13799. DOI:10.1074/jbc.M112.433961&amp;lt;/ref&amp;gt;. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces &amp;lt;ref name=&amp;quot;JBC1&amp;quot;/&amp;gt;. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market &amp;lt;ref name=&amp;quot;businessIn&amp;quot;&amp;gt;Ramsey, L. (2015). One of the world’s blockbuster drugs might not exist if its research hadn&#039;t flopped in a major way. Retrieved from http://www.businessinsider.com/remicade-would-have-failed-as-a-cancer-drug-2015-12&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan &amp;lt;ref name=&amp;quot;FDA&amp;quot;&amp;gt; REMICADE (Infliximab) for IV injection. (2002). ( No. 1242). Malvern, PA: Centocor, INC. &amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6 &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms &amp;lt;ref name=&amp;quot;FDA&amp;quot;/&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α &amp;lt;ref&amp;gt; Grainger, R., &amp;amp; Harrison, A. A. (2007). Infliximab in the treatment of ankylosing spondylitis. Biologics, 1(2), 163-171.&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. These plaques typically appear on the scalp, knees, elbows and lower back &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies &amp;lt;ref&amp;gt; PMID: 19537380 &amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions &amp;lt;ref&amp;gt; National Psoriasis Foundation. (2016). Moderate to severe psoriasis and psoriatic arthritis: Biologic drugs. Retrieved from https://www.psoriasis.org/about-psoriasis/treatments/biologics&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2683580</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2683580"/>
		<updated>2016-10-20T15:18:43Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated Fab and Fc regions&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F &amp;lt;scene name=&#039;74/744162/Loops_tnf/1&#039;&amp;gt;loop residues&amp;lt;/scene&amp;gt; connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions.  &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2683579</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2683579"/>
		<updated>2016-10-20T14:55:17Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). &amp;lt;scene name=&#039;74/744162/Variable_chains_hc/1&#039;&amp;gt;Click here to view separated regions.&amp;lt;/scene&amp;gt;. The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions.  &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2681607</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2681607"/>
		<updated>2016-10-19T13:46:55Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;74/744162/Bio_assembly_1/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions.  &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2680544</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2680544"/>
		<updated>2016-10-17T15:31:00Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744162/Tyr_141_atom/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions.  &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2680543</id>
		<title>Sandbox 9888</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9888&amp;diff=2680543"/>
		<updated>2016-10-17T13:18:38Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: New page: == &amp;#039;&amp;#039;&amp;#039;Remicade (infliximab)&amp;#039;&amp;#039;&amp;#039; ==  &amp;lt;StructureSection load=&amp;#039;4g3y&amp;#039; size=&amp;#039;340&amp;#039; side=&amp;#039;right&amp;#039; caption=&amp;#039;Caption for this structure&amp;#039; scene=&amp;#039;&amp;#039;&amp;gt;  == Structure ==  Remicade (Infliximab) is a chimeri...&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site.&lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications.&lt;br /&gt;
 &lt;br /&gt;
Using the knowledge of TNF-α as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF-α on the market.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt;&lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions.  &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680504</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680504"/>
		<updated>2016-10-13T19:02:08Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;scene name=&#039;74/744116/Test2/1&#039;&amp;gt;&amp;lt;scene name=&#039;74/744116/Bam6_tyr_141/1&#039;&amp;gt;Text To Be Displayed&amp;lt;/scene&amp;gt;&amp;lt;/scene&amp;gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the &amp;lt;scene name=&#039;74/744116/Bam6_tyr_141/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
&lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF- on the market.  &lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680503</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680503"/>
		<updated>2016-10-13T18:16:38Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. This chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  is fused with the constant regions of a human antibody (75%) at the hinge region through a genetic engineering process. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
&lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a hydrophobic interface through amino acid residues such as the Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. These favorable interactions are essential to the complex formed between TNF-α and infliximab Fab.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made the remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
&lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
&lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first receptor specific antibody for TNF- on the market.  &lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. &lt;br /&gt;
&lt;br /&gt;
In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR). Thus, inhibiting the receptor from signaling production of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
&lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680464</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680464"/>
		<updated>2016-10-11T18:19:20Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its &amp;lt;scene name=&#039;74/744116/Tyr_141/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680463</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680463"/>
		<updated>2016-10-11T18:18:42Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;scene name=&#039;74/744116/Tyr_141/3&#039;&amp;gt;Text To Be Displayed&amp;lt;/scene&amp;gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its &amp;lt;scene name=&#039;74/744116/Tyr_141/3&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680462</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680462"/>
		<updated>2016-10-11T18:11:15Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its &amp;lt;scene name=&#039;74/744116/Tyr_141/1&#039;&amp;gt;Tyr-141 side chain&amp;lt;/scene&amp;gt;. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680378</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680378"/>
		<updated>2016-10-09T20:30:10Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-α,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680369</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680369"/>
		<updated>2016-10-08T22:21:32Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680362</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680362"/>
		<updated>2016-10-08T16:30:22Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y_1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:4g3y_1.pdb&amp;diff=2680361</id>
		<title>File:4g3y 1.pdb</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:4g3y_1.pdb&amp;diff=2680361"/>
		<updated>2016-10-08T16:29:07Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: Crystal Structure of TNF-alpha with Infliximab fab (Biological Assembly 1)&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Summary ==&lt;br /&gt;
Crystal Structure of TNF-alpha with Infliximab fab (Biological Assembly 1)&lt;br /&gt;
== Licensing ==&lt;br /&gt;
{{subst:No license from license selector|Don&#039;t know}}&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680360</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680360"/>
		<updated>2016-10-08T16:18:33Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y.pdb&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680359</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680359"/>
		<updated>2016-10-08T16:17:35Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;Structure load=&#039;Insert PDB code or filename here&#039; size=&#039;350&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Insert caption here&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y.pdb1&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680358</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680358"/>
		<updated>2016-10-08T15:28:06Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;370&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680357</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680357"/>
		<updated>2016-10-08T15:27:33Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;480&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680356</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680356"/>
		<updated>2016-10-08T15:26:47Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;380&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680355</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680355"/>
		<updated>2016-10-08T15:19:45Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;4g3y&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680333</id>
		<title>Sandbox 9876</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_9876&amp;diff=2680333"/>
		<updated>2016-10-07T17:14:11Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: New page: == &amp;#039;&amp;#039;&amp;#039;Remicade (infliximab)&amp;#039;&amp;#039;&amp;#039; ==  &amp;lt;StructureSection load=&amp;#039;1stp&amp;#039; size=&amp;#039;340&amp;#039; side=&amp;#039;right&amp;#039; caption=&amp;#039;Caption for this structure&amp;#039; scene=&amp;#039;&amp;#039;&amp;gt; This is a default text for your page &amp;#039;&amp;#039;&amp;#039;Bryan Nguyen...&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:Bryan_Nguyen./Remicade_1&amp;diff=2680332</id>
		<title>User:Bryan Nguyen./Remicade 1</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:Bryan_Nguyen./Remicade_1&amp;diff=2680332"/>
		<updated>2016-10-07T17:12:34Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: Removing all content from page&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:Bryan_Nguyen.&amp;diff=2680329</id>
		<title>User:Bryan Nguyen.</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:Bryan_Nguyen.&amp;diff=2680329"/>
		<updated>2016-10-07T04:25:58Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;*[[User:Bryan Nguyen./Remicade 1]]&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:Bryan_Nguyen.&amp;diff=2680328</id>
		<title>User:Bryan Nguyen.</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:Bryan_Nguyen.&amp;diff=2680328"/>
		<updated>2016-10-07T04:22:40Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;*[[User:Bryan Nguyen./Remicade_1]]&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:Bryan_Nguyen./Remicade_1&amp;diff=2680327</id>
		<title>User:Bryan Nguyen./Remicade 1</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:Bryan_Nguyen./Remicade_1&amp;diff=2680327"/>
		<updated>2016-10-07T04:18:48Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== &#039;&#039;&#039;Remicade (infliximab)&#039;&#039;&#039; == &lt;br /&gt;
&amp;lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:Bryan_Nguyen./Remicade_1&amp;diff=2680326</id>
		<title>User:Bryan Nguyen./Remicade 1</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:Bryan_Nguyen./Remicade_1&amp;diff=2680326"/>
		<updated>2016-10-07T04:17:57Z</updated>

		<summary type="html">&lt;p&gt;Bryan Nguyen.: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Remicade (infliximab) == 2&lt;br /&gt;
&amp;lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;Bryan Nguyen./Remicade 1&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== History of Remicade ==&lt;br /&gt;
&lt;br /&gt;
Originally in search of an immunotherapy drug to combat cancer, Dr. Jan Vilcek and a team of researches made a remarkable discovery of a promising protein, tumor necrosis factor alpha. TNF-,is a cytokine secreted by macrophages to elicit inflammation. Vilcek initially discovered the protein while studying the growth of tumors in transplantable animals, such as murine mice. It was found that this protein could not only block the growth of such tumors, but could even rid the mice completely of cancerous cells. This left many hopeful that TNF could also be employed as a therapeutic agent to fight cancers in humans. &lt;br /&gt;
Beginning human trials, Vilcek and his team caught the attention of several drug companies, especially Centocor. Their hope was to have discovered a means of treating cancer using the body’s own immune system. However, within a few years of trials having been underway, this was not case. Rather, the extraordinary protein they had discovered in 1993 was highly toxic, even at low doses. Although, the study did not result in the desired outcome, the team further researched the use of TNF for other clinical applications. &lt;br /&gt;
Using the knowledge of TNF-as a pro-inflammatory cytokine, Vilcek started exploring the generation of antibodies for the protein. Murine mice were used as a model organism to develop the first monoclonal antibody, A2. This antibody was found to bind to TNF-thus causing the reduction of inflammation in systemic immune responses. The use of TNF inhibitors to treat diseases that were known to induce excessive inflammation, would be the foundation of Remicade. This was an engineered chimeric antibody, created by the combination of mouse and human TNF that allowed for a higher specificity and affinity to the TNF receptor. With the collaborative efforts of Centocor, Remicade became the first drug of its kind on the market. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
Remicade (Infliximab) is a chimeric IgG1 monoclonal antibody consisting of 597 amino acids, weighing 149,000 Daltons. A chimeric monoclonal antibody is produced when the variable regions of a murine antibody (25%)  are combined with the constant regions of a human antibody (75%) at the hinge region. Within the hinge region, intramolecular disulfide bonds stabilize the two fragment antigen binding regions (Fab) to the fragment crystallizable region (Fc). The Fab regions are comprised of both a heavy and light chain, while the Fc region consist of only a heavy chain. Located in the folded Vh and Ch domains of the heavy chain, amino acid residues Glu-1 to Thr-226 are found. In addition, the light chains is composed of residues Asp-1 to Cys-214 that fold into the Vl and Cl domain. The heavy and light chain at the N-terminus form the variable region that functions as a receptor binding site. &lt;br /&gt;
After intravenously injecting Infliximab, the p55 and p75 receptors on TNF-α are neutralized when bound to the drugs high affinity receptor binding sites. The complex formed is stabilized through the vast array of weak interactions between the two proteins, such as hydrogen bonds, salt bridges, and Van der Waal forces. Specifically, TNF-α contributes to the stability by creating a large hydrophobic interface through its Tyr-141 side chain. This interface is formed primarily by the C-D and E-F loop residues connecting the antiparallel 8-stranded Beta sheets. Results of in vitro binding assays revealed the antibody and loops to be interacting through a molecular network.&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
Upon the injection of Remicade into the body, the drug is dispersed throughout the bloodstream and to the tissues. Depending on the patient’s body surface index, the dosage of the drug administered will vary. In determining the proper amount of how much of the drug should be injected, Remicade is able to sufficiently block TNF-α from interacting with the TNF receptors (TNFR) on the target cell, thus inhibiting the induction of IL-1 and IL-6, both of which are pro-inflammatory cytokines. When this occurs, Remicade acts as a competitive inhibitor to TNF-R. If an adequate amount is introduced, the interface will be obstructed, thus preventing TNF-α from participating further in diseases. &lt;br /&gt;
Once the complex forms, it is stabilized by the amino acid residues Gln67–His73 and Gln102–Lys112 of the C-D and E-F loops. Particularly, the weak interactions between the loops and side chains, allows for a stronger binding affinity. (ASK ABOUT ACIDIC CHAIN SUBSTITUTIONS) The strongest interaction between the two proteins is best seen in the peak region in Figure.... This arises when TNF-α is in its active form and exists as a trimer. Although, research has offered some insight into the mechanisms of how Remicade effectively inhibits TNF-α, studies have not shown a clear understanding of the extensive underlying network. Thus, more research into this matter should be pursued.&lt;br /&gt;
&lt;br /&gt;
== Diseases ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Rheumatoid Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Rheumatoid Arthritis is a chronic inflammatory disease that affects the joints of the body, especially those in the hands and feet. Patients with this disease experience severe swelling in the joints that could eventually lead to bone erosion and joint deformity. With the use of Remicade, signs and symptoms can be reduced and the further progression of joint damage can be halted. This ultimately improves physical function and movement in patients enduring moderate to severe active Rheumatoid Arthritis. Often, methotrexate (a chemotherapy drug) is used in addition as part of the treatment plan.&lt;br /&gt;
 &lt;br /&gt;
&amp;lt;b&amp;gt;Crohn’s Disease:&amp;lt;/b&amp;gt; &lt;br /&gt;
Crohn’s disease, also called ileitis, is a chronic inflammatory bowel disease that affects the lining and layers of the digestive tract. Disease activity can be assessed by measuring the levels of TNF-α in stool samples from patients. In the hope of reducing signs and symptoms, patients are prescribed Remicade if they have not responded well to other therapies. Remicade has the ability to reduce the influx of inflammatory cytokines and TNF-α production in the inflamed parts of the intestine. Following treatment, patients exhibit decreased levels of the pro-inflammatory cytokine, IL-6.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ulcerative Colitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Similar to Crohn’s disease, Ulcerative Colitis is a chronic inflammatory bowel disease that causes inflammation in the digestive tract, particularly the sigmoid colon of the large intestine and rectum. Levels of TNF-α in stool samples is a technique used to assess the level of the disease in patients. To promote intestinal healing, Remicade is a drug that can be prescribed to prevent the use of steroids in adults with moderate to severe symptoms. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Ankylosing Spondylitis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Ankylosing Spondylitis is an inflammatory disease affecting the spine and large joints in the body. Symptoms typically begin to appear in early adulthood causing reduced flexibility, eventually leading to a hunched-forward posture. With Remicade, signs and symptoms can be lessened in patients who are experiencing active Ankylosing Spondylitis by inhibiting TNF-α. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Plaque Psoriasis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Plaque psoriasis is the most common form of the disease, appearing as raised, red patches covered with a off-white buildup of dead skin cells. These plaques typically appear on the scalp, knees, elbows and lower back. Remicade has been FDA approved for the treatment of adult patients expressing severe, chronic symptoms. The severity of the disease is ultimately assessed by a physician to determine if Remicade is the right course of action in consideration with other possible therapies.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;b&amp;gt;Psoriatic Arthritis:&amp;lt;/b&amp;gt;&lt;br /&gt;
Psoriatic arthritis is a form of arthritis infecting people who usually have the skin condition plaque psoriasis. This disease cannot be cured but treatment can help with the symptoms. When Remicade is prescribed, symptoms are reduced and further joint damage is prevented. Patients also experience improvement in physical functions. &lt;br /&gt;
&lt;br /&gt;
== Structural highlights ==&lt;br /&gt;
&lt;br /&gt;
This is a sample scene created with SAT to &amp;lt;scene name=&amp;quot;/12/3456/Sample/1&amp;quot;&amp;gt;color&amp;lt;/scene&amp;gt; by Group, and another to make &amp;lt;scene name=&amp;quot;/12/3456/Sample/2&amp;quot;&amp;gt;a transparent representation&amp;lt;/scene&amp;gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Bryan Nguyen.</name></author>
	</entry>
</feed>