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	<id>https://proteopedia.org/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=John+Means</id>
	<title>Proteopedia - User contributions [en]</title>
	<link rel="self" type="application/atom+xml" href="https://proteopedia.org/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=John+Means"/>
	<link rel="alternate" type="text/html" href="https://proteopedia.org/Special:Contributions/John_Means"/>
	<updated>2026-09-16T14:48:25Z</updated>
	<subtitle>User contributions</subtitle>
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	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1592&amp;diff=3461327</id>
		<title>Sandbox Reserved 1592</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1592&amp;diff=3461327"/>
		<updated>2021-10-14T14:13:52Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_JMeans}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Your Heading Here (maybe something like &#039;Structure&#039;)==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;test caption&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#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;
== Function ==&lt;br /&gt;
&lt;br /&gt;
== Disease ==&lt;br /&gt;
&lt;br /&gt;
== Relevance ==&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>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=3446923</id>
		<title>Template:Sandbox Reserved JMeans</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=3446923"/>
		<updated>2021-09-14T02:57:05Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| style=&amp;quot;background-color:#ffffe0;&amp;quot; border=&amp;quot;1&amp;quot; cellpadding=&amp;quot;5&amp;quot;&lt;br /&gt;
| This Sandbox is Reserved from September 14, 2021, through May 31, 2022, for use in the class &#039;&#039;Introduction to Biochemistry&#039;&#039; taught by [[User:John Means]] at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 5 reserved sandboxes ([[Sandbox Reserved 1590]] through [[Sandbox Reserved 1594]]).&lt;br /&gt;
|-&lt;br /&gt;
| To get started:&lt;br /&gt;
* Click the &#039;&#039;edit this page&#039;&#039; tab at the top. &amp;lt;font color=&amp;quot;red&amp;quot;&amp;gt;Save the page after each step, then edit it again.&amp;lt;/font&amp;gt;&lt;br /&gt;
* Click the &#039;&#039;&#039;3D&#039;&#039;&#039; button (when editing, above the wikitext box) to insert Jmol.&lt;br /&gt;
* &#039;&#039;&#039;show&#039;&#039;&#039; the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.&lt;br /&gt;
* Add a description of your scene. Use the buttons above the wikitext box for&#039;&#039;&#039; bold&#039;&#039;&#039;, &#039;&#039;italics&#039;&#039;, [[#|links]], &amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;b&amp;gt;headlines&amp;lt;/b&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;, etc.&lt;br /&gt;
More help: [[Help:Editing]].&lt;br /&gt;
For an example of a student Proteopedia page, please see [[Photosystem II]], [[Tetanospasmin]], or [[Guanine riboswitch]].&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:John_Means&amp;diff=3443440</id>
		<title>User:John Means</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:John_Means&amp;diff=3443440"/>
		<updated>2021-09-02T16:30:11Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;John A. Means, Ph.D. is a Professor of Chemistry at the University of Rio Grande, in Rio Grande, Ohio, USA. He received his B.S. in Chemistry from Capital University, his M.S. in Medicinal Chemistry from The Ohio State University and his Ph.D. in Chemistry (concentration in Biochemistry) from Ohio University. John is interested in nucleic acid structure and small molecule interactions with nucleic acids.&lt;br /&gt;
&lt;br /&gt;
*[[User:John Means/Sandbox 1]]&lt;br /&gt;
&lt;br /&gt;
*[[Template:Sandbox_Reserved_JMeans]]&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1578&amp;diff=3122469</id>
		<title>Sandbox Reserved 1578</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1578&amp;diff=3122469"/>
		<updated>2019-12-04T13:43:58Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_JMeans}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==SAM Riboswitch==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;2gis&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;SAM Riboswitch&#039; scene=&#039;&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Overview==&lt;br /&gt;
&lt;br /&gt;
S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.&amp;lt;ref name=&amp;quot;ref1&amp;quot;&amp;gt;PMID:16810258&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structural Highlights ==&lt;br /&gt;
&lt;br /&gt;
The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3&#039; side of another helix surrounding the SAM ligand, as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The SAM ligand is bound within a pocket created by the &amp;lt;scene name=&#039;82/824623/Helix_interaction/2&#039;&amp;gt;Helix Interaction&amp;lt;/scene&amp;gt; (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring.  Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix. &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
The adenine ring of SAM is the central position between five nucleotides.  The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position &amp;lt;scene name=&#039;82/824623/Nitrogenous_base_interactions/3&#039;&amp;gt;Nucleotide Interaction&amp;lt;/scene&amp;gt;(orange). &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function == &lt;br /&gt;
&lt;br /&gt;
Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target.  Genetic regulation by RNA is often used in bacterial cells.  In the use of the SAM riboswitch, the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed previously hold the ligand in place for productive binding, and also folds around the tertiary RNA once binding takes place.  Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression. &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
(1) 	Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1578&amp;diff=3118841</id>
		<title>Sandbox Reserved 1578</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1578&amp;diff=3118841"/>
		<updated>2019-12-04T02:54:40Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_JMeans}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==SAM Riboswitch==&lt;br /&gt;
&lt;br /&gt;
==Overview==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;2gis&#039; size=&#039;350&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;SAM Riboswitch&#039; scene=&#039;SAM Riboswitch&#039; /&amp;gt;&lt;br /&gt;
S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.&amp;lt;ref name=&amp;quot;ref1&amp;quot;&amp;gt;PMID:16810258&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structural Highlights ==&lt;br /&gt;
&lt;br /&gt;
The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3&#039; side of another helix surrounding the SAM ligand, as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The SAM ligand is bound within a pocket created by the &amp;lt;scene name=&#039;82/824623/Helix_interaction/2&#039;&amp;gt;Helix Interaction&amp;lt;/scene&amp;gt; (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring.  Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix. &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
The adenine ring of SAM is the central position between five nucleotides.  The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position &amp;lt;scene name=&#039;82/824623/Nitrogenous_base_interactions/3&#039;&amp;gt;Nucleotide Interaction&amp;lt;/scene&amp;gt;(orange). &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function == &lt;br /&gt;
&lt;br /&gt;
Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target.  Genetic regulation by RNA is often used in bacterial cells.  In the use of the SAM riboswitch, the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed previously hold the ligand in place for productive binding, and also folds around the tertiary RNA once binding takes place.  Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression. &amp;lt;ref name=&amp;quot;ref1&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
(1) 	Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1597&amp;diff=3104676</id>
		<title>Sandbox Reserved 1597</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1597&amp;diff=3104676"/>
		<updated>2019-10-30T16:02:31Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_JMeans}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Your Heading Here (maybe something like &#039;Structure&#039;)==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;1n53&#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;&#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;
== Function ==&lt;br /&gt;
This is test.&amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Disease ==&lt;br /&gt;
&lt;br /&gt;
== Relevance ==&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>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=3088398</id>
		<title>Template:Sandbox Reserved JMeans</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=3088398"/>
		<updated>2019-09-19T14:58:09Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| style=&amp;quot;background-color:#ffffe0;&amp;quot; border=&amp;quot;1&amp;quot; cellpadding=&amp;quot;5&amp;quot;&lt;br /&gt;
| This Sandbox is Reserved from September 23, 2019, through May 31, 2020, for use in the class &#039;&#039;Introduction to Biochemistry&#039;&#039; taught by [[User:John Means]] at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 22 reserved sandboxes ([[Sandbox Reserved 1091]] through [[Sandbox Reserved 1112]]).&lt;br /&gt;
|-&lt;br /&gt;
| To get started:&lt;br /&gt;
* Click the &#039;&#039;edit this page&#039;&#039; tab at the top. &amp;lt;font color=&amp;quot;red&amp;quot;&amp;gt;Save the page after each step, then edit it again.&amp;lt;/font&amp;gt;&lt;br /&gt;
* Click the &#039;&#039;&#039;3D&#039;&#039;&#039; button (when editing, above the wikitext box) to insert Jmol.&lt;br /&gt;
* &#039;&#039;&#039;show&#039;&#039;&#039; the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.&lt;br /&gt;
* Add a description of your scene. Use the buttons above the wikitext box for&#039;&#039;&#039; bold&#039;&#039;&#039;, &#039;&#039;italics&#039;&#039;, [[#|links]], &amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;b&amp;gt;headlines&amp;lt;/b&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;, etc.&lt;br /&gt;
More help: [[Help:Editing]].&lt;br /&gt;
For an example of a student Proteopedia page, please see [[Photosystem II]], [[Tetanospasmin]], or [[Guanine riboswitch]].&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=2765243</id>
		<title>Template:Sandbox Reserved JMeans</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=2765243"/>
		<updated>2017-09-14T15:30:12Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| style=&amp;quot;background-color:#ffffe0;&amp;quot; border=&amp;quot;1&amp;quot; cellpadding=&amp;quot;5&amp;quot;&lt;br /&gt;
| This Sandbox is Reserved from September 25, 2017, through May 7, 2018, for use in the class &#039;&#039;Introduction to Biochemistry&#039;&#039; taught by [[User:John Means]] at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 9 reserved sandboxes ([[Sandbox Reserved 1091]] through [[Sandbox Reserved 1100]]).&lt;br /&gt;
|-&lt;br /&gt;
| To get started:&lt;br /&gt;
* Click the &#039;&#039;edit this page&#039;&#039; tab at the top. &amp;lt;font color=&amp;quot;red&amp;quot;&amp;gt;Save the page after each step, then edit it again.&amp;lt;/font&amp;gt;&lt;br /&gt;
* Click the &#039;&#039;&#039;3D&#039;&#039;&#039; button (when editing, above the wikitext box) to insert Jmol.&lt;br /&gt;
* &#039;&#039;&#039;show&#039;&#039;&#039; the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.&lt;br /&gt;
* Add a description of your scene. Use the buttons above the wikitext box for&#039;&#039;&#039; bold&#039;&#039;&#039;, &#039;&#039;italics&#039;&#039;, [[#|links]], &amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;b&amp;gt;headlines&amp;lt;/b&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;, etc.&lt;br /&gt;
More help: [[Help:Editing]].&lt;br /&gt;
For an example of a student Proteopedia page, please see [[Photosystem II]], [[Tetanospasmin]], or [[Guanine riboswitch]].&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=2765232</id>
		<title>Template:Sandbox Reserved JMeans</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=2765232"/>
		<updated>2017-09-14T15:03:08Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| style=&amp;quot;background-color:#ffffe0;&amp;quot; border=&amp;quot;1&amp;quot; cellpadding=&amp;quot;5&amp;quot;&lt;br /&gt;
| This Sandbox is Reserved from September 25, 2017, through May 7, 2018, for use in the class &#039;&#039;Introduction to Biochemistry&#039;&#039; taught by [[User:John Means]] at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 9 reserved sandboxes ([[Sandbox Reserved ____]] through [[Sandbox Reserved ____]]).&lt;br /&gt;
|-&lt;br /&gt;
| To get started:&lt;br /&gt;
* Click the &#039;&#039;edit this page&#039;&#039; tab at the top. &amp;lt;font color=&amp;quot;red&amp;quot;&amp;gt;Save the page after each step, then edit it again.&amp;lt;/font&amp;gt;&lt;br /&gt;
* Click the &#039;&#039;&#039;3D&#039;&#039;&#039; button (when editing, above the wikitext box) to insert Jmol.&lt;br /&gt;
* &#039;&#039;&#039;show&#039;&#039;&#039; the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.&lt;br /&gt;
* Add a description of your scene. Use the buttons above the wikitext box for&#039;&#039;&#039; bold&#039;&#039;&#039;, &#039;&#039;italics&#039;&#039;, [[#|links]], &amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;b&amp;gt;headlines&amp;lt;/b&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;, etc.&lt;br /&gt;
More help: [[Help:Editing]].&lt;br /&gt;
For an example of a student Proteopedia page, please see [[Photosystem II]], [[Tetanospasmin]], or [[Guanine riboswitch]].&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:John_Means/Sandbox_1&amp;diff=2497086</id>
		<title>User:John Means/Sandbox 1</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:John_Means/Sandbox_1&amp;diff=2497086"/>
		<updated>2015-11-04T02:18:15Z</updated>

		<summary type="html">&lt;p&gt;John Means: Removing all content from page&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:John_Means/Sandbox_1&amp;diff=2497085</id>
		<title>User:John Means/Sandbox 1</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:John_Means/Sandbox_1&amp;diff=2497085"/>
		<updated>2015-11-04T01:53:07Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;StructureSection load=&#039;1iH5&#039; size=&#039;350&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;The 1 chain structure of human Aquaporin 1  [[1ih5]]&#039;  scene=&#039;Insert Optional Scene Name Here&#039; /&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
== Aquaporins ==&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
Aquaporin-1 (AQP1) was first discovered in human red blood cell membranes by Gheorghe Benga&#039;s research group in 1986.&amp;lt;ref&amp;gt;PMID: 22705445 &amp;lt;/ref&amp;gt; However, it was only known to be a novel protein and its function was unknown. Initially AQP1 was coined CHIP28 for &#039;&#039;CH&#039;&#039;annel forming &#039;&#039;I&#039;&#039;ntegral membrane &#039;&#039;P&#039;&#039;rotein of &#039;&#039;28&#039;&#039; kDa. It was&#039;nt until 1991, Peter Agres research group discovered the functional characteristics of AQP1. In 1993, CHIP23 was renamed AQP1. Since then, 12 other isoforms of aquaporin-1 have been discovered and each have been classified under the family known as Aquaporins.&amp;lt;ref name=&amp;quot;Cardiac&amp;quot;&amp;gt; PMID: 24158693 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Aquaporins are integral membrane proteins that specialize in the regulation of cellular water flow across the cell membrane.&amp;lt;ref&amp;gt;PMID: 22334691 &amp;lt;/ref&amp;gt; This process is vital for any living organism to sustain proper physiological conditions and aquaporins are necessary to sustain this process (i.e. osmosis alone could not provide a sufficient flow of water). Extensive research on the function of aquaporins have been implemented into many separate types of cell membranes. Such membranes are from brain cells, kidney cells, muscle cells, red blood cells, and heart cells. &lt;br /&gt;
&lt;br /&gt;
Water selective aquaporins are AQP1, -2, -4, -5, -6, -8, -12, and -0. A subgroup of aquaporins called aquaglycerporins allow the passage of small solutes such as glycerol, urea, and ammonia. Aquaglyceroporins are AQP3, -7, -9, and -10.&amp;lt;ref name=&amp;quot;Cardiac&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Aquaporin-1 Structure ==&lt;br /&gt;
&lt;br /&gt;
Aquaporin-1 is an integral membrane protein that is considered to have an &amp;quot;open&amp;quot; structure. Despite being &amp;quot;open&amp;quot;, AQP1 has a high selectivity for the bidirectional transport of water, that even excludes small molecules such as hydrogen ions. AQP1 is formed as a tetramer &#039;&#039;in vivo&#039;&#039;, with each AQP1 monomer unit capable of transportation at a rate of ~2 trillion water molecules per second.&amp;lt;ref name=&amp;quot;structure&amp;quot;&amp;gt; PMID: 11171962 &amp;lt;/ref&amp;gt; &lt;br /&gt;
&lt;br /&gt;
[[Image:Aquaporin-Sideview.png|thumb|350px|left|Side view of AQP1 tetramer. &lt;br /&gt;
Available from: http://upload.wikimedia.org/wikipedia/commons/a/a5/Aquaporin-Sideview.png]]&lt;br /&gt;
&lt;br /&gt;
An AQP1 monomer unit contains six highly tilted transmembrane α-helices and two internal α-helices, oriented in the form of a barrel. The transmembrane α-helices thread through the membrane so as to expose both the N- and the C-terminus to the inner cytoplasm. The aqueous pathway within the monomer unit is characterized by a narrow curvilinear pore that is ~4.0Å in diameter, ~18Å in length, and bends ~25 degrees as it transverses the membrane.&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt; The curvilinear pore is a size selective pathway for water that excludes other larger and smaller molecules. The entrances to the aqueous pathway are mostly lined with polar and charged residues. Conversely, the interior of the aqueous pathway is mostly constituted by nonpolar residues. This feature allows for a relatively noninteracting pathway for the diffusion of water. &lt;br /&gt;
&lt;br /&gt;
The N- and C-terminal halves of AQP1 are tandem repeats that contain a conserved &amp;lt;scene name=&#039;56/560863/Npa/3&#039;&amp;gt;Asn-Pro-Ala (NPA)&amp;lt;/scene&amp;gt; tripeptide sequence.&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt; Each terminal half is composed of three tilted transmembrane α-helices and a short α-helix adjacent to the conserved NPA motif. The two halves are connected through transmembrane 3 (TM3) and TM4 by a &amp;lt;scene name=&#039;56/560863/Interhelix_chain/1&#039;&amp;gt;long interhelix chain&amp;lt;/scene&amp;gt;. The location of the two NPA tripeptide sequences define the apex of the curvilinear pathway (N76 &amp;amp; N192), which is located about the center of the membrane. This orientation of helices allows for a sufficient amount of noncovalent interactions to induce stability. Interactions between helices are dominantly hydrophobic. However, hydrogen-bond interactions have also been suggested to increase stability. &lt;br /&gt;
&lt;br /&gt;
AQP1 takes the form of a tetramer &#039;&#039;in vivo&#039;&#039;. The Quaternary interactions between monomeric units are both hydrophobic and polar. Within the membrane, monomer interactions are dominantly hydrophobic. Whereas hydrogen-bonding dominates nocovalent interactions outside the membrane. The transmembrane α-helices of each monomer are oriented so &amp;lt;scene name=&#039;56/560863/Tm1_2_4_5/1&#039;&amp;gt;TM1, TM2, TM4, and TM5 &amp;lt;/scene&amp;gt;define the interior of the AQP1 monomer (i.e. these helices face the other monomer units). &amp;lt;scene name=&#039;56/560863/Tm3_6/1&#039;&amp;gt;TM3 and TM6&amp;lt;/scene&amp;gt; are defined as the membrane exposed exterior face.&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Aquaporin-1 Regulation ==&lt;br /&gt;
&lt;br /&gt;
Aquaporin channels may be subject to intense short term regulation via signal transduction. Transducers act as extracellular signal molecules that induce a response from membrane proteins. Protein Kinase C (PKC) has been documented as a common signal transducer among the aquaporins. One study suggests the positive relationship between PKC and AQP1.&amp;lt;ref&amp;gt;PMID: 17522053 &amp;lt;/ref&amp;gt; In the presence of PKC, AQP1 was reported to have increased aqueous permeability. Phosphorylation of the amino acid &amp;lt;scene name=&#039;56/560863/Thr157/3&#039;&amp;gt;Thr157&amp;lt;/scene&amp;gt; on the AQP1 protein by PKC is attributed to the increased permeability. The increased activity of AQP1 in the presence of PKC may contribute to the stimulation of physiological processes that are modulated by AQP1 such as endothelial permeability, angiogenesis, and urea concentration.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=User:John_Means&amp;diff=2487329</id>
		<title>User:John Means</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=User:John_Means&amp;diff=2487329"/>
		<updated>2015-09-18T13:55:52Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;John A. Means, Ph.D. is an Associate Professor of Chemistry at the University of Rio Grande, in Rio Grande, Ohio, USA. He received his B.S. in Chemistry from Capital University, his M.S. in Medicinal Chemistry from The Ohio State University and his Ph.D. in Chemistry (concentration in Biochemistry) from Ohio University. John is interested in nucleic acid structure and small molecule interactions with nucleic acids.&lt;br /&gt;
&lt;br /&gt;
*[[User:John Means/Sandbox 1]]&lt;br /&gt;
&lt;br /&gt;
*[[Template:Sandbox_Reserved_JMeans]]&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
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		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=2487328"/>
		<updated>2015-09-18T13:53:00Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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| This Sandbox is Reserved from September 21, 2015, through December 18, 2015, for use in the class &#039;&#039;Introduction to Biochemistry&#039;&#039; taught by [[User:John Means]] at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes ten reserved sandboxes (901 through 912).&lt;br /&gt;
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		<author><name>John Means</name></author>
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	<entry>
		<id>https://proteopedia.org/index.php?title=Hairpin_Ribozyme&amp;diff=2487327</id>
		<title>Hairpin Ribozyme</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Hairpin_Ribozyme&amp;diff=2487327"/>
		<updated>2015-09-18T13:47:07Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&lt;div&gt;&amp;lt;StructureSection load=&#039;1m5k&#039; size=&#039;350&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;The hairpin ribozyme (red) with substrate (blue) and ribonucleoprotein (green) [[1m5k]]&#039;  scene=&#039;56/560862/Ribozyme_substrate_and_protein/1&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Overview==&lt;br /&gt;
The &amp;lt;scene name=&#039;56/560862/Ribozyme_substrate_and_protein/1&#039;&amp;gt;hairpin ribozyme&amp;lt;/scene&amp;gt; is a member of a small family of RNA endonucleases that includes hammerhead, hepatitis delta, and Neurospora VS.&amp;lt;ref name=&amp;quot;Shippy&amp;quot;&amp;gt;PMID: 10554775&amp;lt;/ref&amp;gt;  Endonucleases are enzymes that cleave phosphodiester bonds within polynucleotide chains.  This group of endonucleases cleave RNA substrates in a reversible reaction that generates a 2&#039;, 3&#039;-cyclic phosphate and a 5&#039;-hydroxyl termini.&amp;lt;ref name=&amp;quot;Shippy&amp;quot;/&amp;gt;&amp;lt;ref&amp;gt;PMID: 10715200&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The hairpin ribozyme was discovered in the negative strand of the tobacco ringspot virus (TRSV) satellite RNA.&amp;lt;ref&amp;gt;PMID: 22131309&amp;lt;/ref&amp;gt;  Study of hairpin ribozyme reaction mechanisms provided early evidence that ribozymes are able to exploit a variety of strategies, just like protein enzymes.  But, the hairpin ribozyme has a unique characteristic.  Unlike other ribozymes, the hairpin ribozyme does not require metal ions for cleavage or ligation of substrate RNA, though it does use metal ions to facilitate domain interactions.&amp;lt;ref name=&amp;quot;Walter&amp;quot;&amp;gt;PMID: 9667918&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
The secondary structure of the hairpin ribozyme contains two independently folding domains, called&lt;br /&gt;
&amp;lt;scene name=&#039;56/560862/Domain_a_and_domain_b/1&#039;&amp;gt;A (green) and B (yellow)&amp;lt;/scene&amp;gt;.  In each domain there is an internal loop flanked by two helices (H1 and H2 in domain A and H3 and H4 in domain B).  The RNA substrate is bound in domain A through Watson-Crick base pairs in H1 and H2.  Once bound to domain A, the substrate is reversibly cleaved.  Linkers of varying lengths were inserted between the 5&#039; end of the substrate and the 3&#039; end of the ribozyme in order to test what proximity is preferred by the two domains.  The results of the test showed that the two domains prefer to be relatively close to one another and use H2 and H3 as a sort of hinge.  In the naturally occurring hairpin ribozyme, this hinge is occupied by a four-way junction, which is believed to regulate inter-domain interactions by alternative stacking of helices.&amp;lt;ref name=&amp;quot;Walter&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Catalysis==&lt;br /&gt;
In the transition state, the hairpin ribozyme demonstrates coordinate bonding.  The substrate binds to the 2&#039; and 3&#039; oxygens of nucleotide -1 and the 5&#039; oxygen of nucleotide +1.  This bonding creates a large amount of electron density, which is very important to the mechanism.  If even one of the coordinate bonds is absent, the electron density feature is absent as well.  When the hairpin ribozyme is bound to a substrate that is entirely RNA, the electron density is made up of a mixture of the cleaved and ligated substrate.  This is because the ribozyme catalyzes both the cleavage reaction and the reverse ligation.&amp;lt;ref name=&amp;quot;Rupert&amp;quot;&amp;gt;PMID: 12376595&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Crystal structures of the transition state, precursor, and product indicate that the active site remains in a fairly fixed position.  The lone motion occurs between the &amp;lt;scene name=&#039;56/560862/Scissile_phosphate/1&#039;&amp;gt;scissile phosphate&amp;lt;/scene&amp;gt; and the ribose of nucleotide -1.  The ribose undergoes a change in puckering when its 2&#039; oxygen attacks the phosphate and a five membered 2&#039;, 3&#039; phosphate is formed.&amp;lt;ref name=&amp;quot;Rupert&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Hydrogen bonding is a major contributor to the catalytic process.  In the precursor, the ribozyme forms two hydrogen bonds.  One is between the nucleobase of G8 and the 2&#039;-OH nucleophile and the other is between the nucleobase of G8 and one of the phosphate oxygens.  In the transition state, five hydrogen bonds are formed.  Those H-bonds occur between the nucleobases of &amp;lt;scene name=&#039;56/560862/G8_and_a9/1&#039;&amp;gt;G8, A9&amp;lt;/scene&amp;gt;, and A38 and the oxygens of the substrate.  In the product, the nucleobases of G8 and A38 make three hydrogen bonds.  Two are formed to the cyclic phosphate and the other is to 5&#039;-OH leaving group.&amp;lt;ref name=&amp;quot;Rupert&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Kinetics==&lt;br /&gt;
There are at least four steps in the reaction pathway of the hairpin ribozyme.  They are: (1) substrate binding to ribozyme, (2) cleavage in the ribozyme-substrate complex, (3) release of 5&#039; products, and (4) release of 3&#039; products.  The rates and equilibrium constants of these individual steps have been studied.  Substrate binding by the naturally occurring hairpin ribozyme can reach a minimum of 6x10&amp;lt;sup&amp;gt;6&amp;lt;/sup&amp;gt; M&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; min&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and modified versions can reach maximums of 5x10&amp;lt;sup&amp;gt;8&amp;lt;/sup&amp;gt; M&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; min&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.  The cleavage rate is significantly higher than the dissociation rate, meaning cleavage of bound substrate is highly favored over dissociation.  Tests have also shown that the hairpin ribozyme has a biphasic cleavage.  The fast phase is due to the ribozyme-substrate complex being folded correctly and the slow phase is due to an inactive conformer with H2 and H3 coaxially stacked.&amp;lt;ref&amp;gt;PMID: 9153212&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==3D structures of ribozyme==&lt;br /&gt;
[[Ribozyme]]&lt;br /&gt;
&lt;br /&gt;
==References==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=1839904</id>
		<title>Template:Sandbox Reserved JMeans</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Template:Sandbox_Reserved_JMeans&amp;diff=1839904"/>
		<updated>2013-09-06T15:02:03Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
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| This Sandbox is Reserved from September 6, 2013, through December 16, 2013, for use in the class &#039;&#039;Introduction to Biochemistry&#039;&#039; taught by [[User:John Means]] at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes ten reserved sandboxes (901 through 910).&lt;br /&gt;
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		<author><name>John Means</name></author>
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	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329770</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329770"/>
		<updated>2011-12-08T20:10:24Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
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&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;..&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt; MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name= &amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein. There are several nitrogens that form rings that have an iron placed in the center. There is also a lone calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;alpha helices and beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr (Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by &#039;&#039;Gonococci&#039;&#039;. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure &#039;&#039;Gonococci&#039;&#039; has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it is so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of &amp;quot;Regulation of MtrF Expression in &#039;&#039;Neisseria gonorrhoeae&#039;&#039; and Its Role in High-Level Antimicrobial Resistance&amp;quot;.&amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt; In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when &#039;&#039;Gonococci&#039;&#039; are grown under inducing conditions.&lt;br /&gt;
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==References== &lt;br /&gt;
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&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1329765</id>
		<title>Sandbox Reserved 384</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1329765"/>
		<updated>2011-12-08T17:09:47Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;2qkh&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Glucose-dependant insulinotropic polypeptide receptor, [[2qkh]]&#039; scene=&#039;&#039; /&amp;gt;&lt;br /&gt;
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=Glucose-dependent Insulinotropic Polypeptide Receptor=&lt;br /&gt;
==Background==&lt;br /&gt;
Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a transmembrane protein which is responsible for boosting glucose-induced insulin production. The transcription of this protein is positively controlled by glucose molecules; GIPR is expressed in higher levels when glucose is in higher concentration. The receptor is a multispan membrane-bound protein (shown in blue) consisting of an alpha helix, half twist helices, and beta sheets bound in several locations with disulfide bonds within itself. The ligand which binds to GIPR is glucose-dependent insulinotropic polypeptide (GIP), also known as gastric inhibitory polypeptide (shown in green). GIP is an alpha helical endogenous polypeptide hormone which is released upon the ingestion of food, specifically the carbohydrate glucose. &lt;br /&gt;
&lt;br /&gt;
===Molecular Function===&lt;br /&gt;
The purpose of the receptor is to bind glucose-dependent insulinotropic polypeptide (GIP) in the presence of glucose. This causes a chain reaction that increases secretion of insulin molecules. GIP binds to GIPR though &amp;lt;scene name=&#039;Sandbox_Reserved_384/Hydrophobics/1&#039;&amp;gt;hydrophobic interactions&amp;lt;/scene&amp;gt; and causes the release of G protein-coupled receptors, which in turn causes an enzymatic cascade resulting in the increased secretion of insulin. This occurs in the pancreatic islet beta-cells. It is likely that the cause of type 2 diabetes is due to the inability of GIP to bind properly to GIPR.&amp;lt;ref&amp;gt;PMID:11334402&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Ongoing Research===&lt;br /&gt;
The significance of this receptor makes it a prime target for diabetes research. Incretins are a class of biological molecules that act like gastrointestinal hormones. One such example is glucagon-like peptide-1 (GLP-1), which works with GIP to regulate the body&#039;s insulin levels. Synthetic versions of this peptide hormone have been made to treat people with type-2 diabetes. It works by stimulating GIP production as well as insulin secretion causing the body to properly regulate its blood glucose levels like someone without diabetes. The benefit of synthetic GLP-1 is that it is not protein and so would not be degraded as easily therefore prolonging the benefits of the drug. One such example is Byetta&amp;lt;ref&amp;gt;&amp;quot;Byetta.&amp;quot; BYETTA (exenatide) Injection | Welcome to BYETTA.com. Amylin Pharmaceuticals, Inc., 2011. Web. 02 Dec. 2011. &amp;lt;http://www.byetta.com/Pages/index.aspx&amp;gt;&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
[[Image:F3.large.jpg|thumb|400px|left|GIP-induced Pathway.&amp;lt;ref&amp;gt;PMID:12475913&amp;lt;/ref&amp;gt;]]&lt;br /&gt;
{{Clear}}&lt;br /&gt;
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===References=== &lt;br /&gt;
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&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329751</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329751"/>
		<updated>2011-12-08T14:13:07Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID:15148138&amp;lt;/ref&amp;gt; &lt;br /&gt;
&lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;PMID: 1916765&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID: 19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref name=&amp;quot;structure&amp;quot;&amp;gt;PMID: 21097933&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt;&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;PMID: 16650084&amp;lt;/ref&amp;gt;&lt;br /&gt;
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==References== &lt;br /&gt;
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&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1329750</id>
		<title>Sandbox Reserved 387</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1329750"/>
		<updated>2011-12-08T13:50:27Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;3RJ1&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Mediator&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Mediator ==&lt;br /&gt;
The mediator, found in the yeast &#039;&#039;S. cerevisiae&#039;&#039;, connects repressors and activators bound to regulatory DNA with RNA polymerase II (Pol II). As a result, the mediator is an important regulator of eukaryotic transcription.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt; Also, mediator is currently being studied because of its ability and role to regulate gene expression.&amp;lt;ref&amp;gt;PMID: 20299225 &amp;lt;/ref&amp;gt; Mediator is in the form of three main modules, which are the tail, arm, and head. The &amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt; of the mediator is split into three domains that go through significant conformational changes, and it interacts with the Rpb7 and Rpb4 subunits of Pol II and TATA binding protein subunit of transcription factor TFIID.&amp;lt;ref name=&amp;quot;nature&amp;quot;&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt;&lt;br /&gt;
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== Structure ==&lt;br /&gt;
The &amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt; of mediator from &#039;&#039;S.cerevisiae&#039;&#039; is made of seven subunits which are Med22(Srb6), Med20(Srb2), Med18(Srb5), Med17(Srb4), Med11, Med6, and Med8.&amp;lt;ref name=&amp;quot;nature&amp;quot; /&amp;gt; Of these subunits, Med11, Med17(Srb4), and Med22(Srb6) make the mini-head of the head module. The subunits of the core-head plus the subunits of the mini-head are what make up full head structure. The structure shows the three domains: the neck, which is shown by pink helices, the fixed jaw, which is shown by mostly pink helices and a few yellow beta sheets, and the movable jaw, which is shown by mostly yellow beta sheets and a few pink helices.&lt;br /&gt;
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== References ==&lt;br /&gt;
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&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1329749</id>
		<title>Sandbox Reserved 387</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1329749"/>
		<updated>2011-12-08T13:43:04Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;3RJ1&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Mediator&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
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== Mediator==&lt;br /&gt;
The mediator, found in the yeast &#039;&#039;S. cerevisiae&#039;&#039;, connects repressors and activators bound to regulatory DNA with RNA polymerase II (Pol II). As a result, the mediator is an important regulator of eukaryotic transcription.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt; Also, mediator is currently being studied because of its ability and role to regulate gene expression.&amp;lt;ref&amp;gt;PMID: 20299225 &amp;lt;/ref&amp;gt; Mediator is in the form of three main modules, which are the tail, arm, and head. The &amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt; of the mediator is split into three domains that go through significant conformational changes, and it interacts with the Rpb7 and Rpb4 subunits of Pol II and TATA binding protein subunit of transcription factor TFIID.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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  &lt;br /&gt;
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== Structure ==&lt;br /&gt;
The &amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt; of mediator from &#039;&#039;S.cerevisiae&#039;&#039; is made of seven subunits which are Med22(Srb6), Med20(Srb2), Med18(Srb5), Med17(Srb4), Med11, Med6, and Med8.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt; Of these subunits, Med11, Med17(Srb4), and Med22(Srb6) make the mini-head of the head module. The subunits of the core-head plus the subunits of the mini-head are what make up full head structure. The structure shows the three domains: the neck, which is shown by pink helices, the fixed jaw, which is shown by mostly pink helices and a few yellow beta sheets, and the movable jaw, which is shown by mostly yellow beta sheets and a few pink helices.&lt;br /&gt;
&lt;br /&gt;
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== References ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1329719</id>
		<title>Sandbox Reserved 387</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1329719"/>
		<updated>2011-12-07T20:05:41Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
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&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3RJ1&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;Mediator&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
== Mediator==&lt;br /&gt;
The mediator, found in the yeast &#039;&#039;S. cerevisiae&#039;&#039;, connects repressors and activators bound to regulatory DNA with RNA polymerase II (Pol II). As a result, the mediator is an important regulator of eukaryotic transcription.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt; Also, mediator is currently being studied because of its ability and role to regulate gene expression.&amp;lt;ref&amp;gt;PMID: 20299225 &amp;lt;/ref&amp;gt; Mediator is in the form of three main modules, which are the tail, arm, and head. The &amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt; of the mediator is split into three domains that go through significant conformational changes, and it interacts with the Rpb7 and Rpb4 subunits of Pol II and TATA binding protein subunit of transcription factor TFIID.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
  &lt;br /&gt;
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== Structure ==&lt;br /&gt;
The &amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt; of mediator from &#039;&#039;S.cerevisiae&#039;&#039; is made of seven subunits which are Med22(Srb6), Med20(Srb2), Med18(Srb5), Med17(Srb4), Med11, Med6, and Med8.&amp;lt;ref&amp;gt;PMID: 21725323 &amp;lt;/ref&amp;gt; Of these subunits, Med11, Med17(Srb4), and Med22(Srb6) make the mini-head of the head module. The subunits of the core-head plus the subunits of the mini-head are what make up full head structure. The structure shows the three domains: the neck, which is shown by pink helices, the fixed jaw, which is shown by mostly pink helices and a few yellow beta sheets, and the movable jaw, which is shown by mostly yellow beta sheets and a few pink helices.&lt;br /&gt;
&lt;br /&gt;
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== References ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329578</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329578"/>
		<updated>2011-12-07T17:39:21Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
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== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein. There are several nitrogens that form rings that have an iron placed in the center. There is also a lone calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;alpha helices and beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr (Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by &#039;&#039;Gonococci&#039;&#039;. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure &#039;&#039;Gonococci&#039;&#039; has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it is so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of &amp;quot;Regulation of MtrF Expression in &#039;&#039;Neisseria gonorrhoeae&#039;&#039; and Its Role in High-Level Antimicrobial Resistance&amp;quot;.&amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt; In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when &#039;&#039;Gonococci&#039;&#039; are grown under inducing conditions.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329568</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329568"/>
		<updated>2011-12-07T17:37:56Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein. There are several nitrogens that form rings that have an iron placed in the center. There is also a lone calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;alpha helices and beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr (Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by &#039;&#039;Gonococci&#039;&#039;. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure &#039;&#039;Gonococci&#039;&#039; has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it’s so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of &amp;quot;Regulation of MtrF Expression in &#039;&#039;Neisseria gonorrhoeae&#039;&#039; and Its Role in High-Level Antimicrobial Resistance&amp;quot;.&amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt; In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when &#039;&#039;Gonococci&#039;&#039; are grown under inducing conditions.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329565</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329565"/>
		<updated>2011-12-07T17:36:36Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein. There are several nitrogens that form rings that have an iron placed in the center. There is also a lone calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;alpha helices and beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr (Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by &#039;&#039;Gonococci&#039;&#039;. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure &#039;&#039;Gonococci&#039;&#039; has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it’s so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of &amp;quot;Regulation of MtrF Expression in &#039;&#039;Neisseria gonorrhoeae&#039;&#039; and Its Role in High-Level Antimicrobial Resistance&amp;quot;.&amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt; In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when gonococci are grown under inducing conditions.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329555</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329555"/>
		<updated>2011-12-07T17:31:48Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein. There are several nitrogens that form rings that have an iron placed in the center. There is also a lone calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;alpha helices and beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr(Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by &#039;&#039;Gonococci&#039;&#039;. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure gonococci has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it’s so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of Regulation of mtrF Expression in Neisseria Gonorrhoeae and Its Role in High-Level Antimicrobial Resistance. In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when gonococci are grown under inducing conditions. &amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329549</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329549"/>
		<updated>2011-12-07T17:29:06Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein, there are several Nitrogens that form rings that have an Iron placed in the center, there is also a lone Calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;alpha helices and beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD Gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr(Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by gonococci. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure gonococci has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it’s so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of Regulation of mtrF Expression in Neisseria Gonorrhoeae and Its Role in High-Level Antimicrobial Resistance. In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when gonococci are grown under inducing conditions. &amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329548</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329548"/>
		<updated>2011-12-07T17:28:31Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca. Oxygen is the most abundant element and is spread out through the entire protein, there are several Nitrogens that form rings that have an Iron placed in the center, there is also a lone Calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;Alpha Helices and Beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD Gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr(Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by gonococci. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure gonococci has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it’s so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of Regulation of mtrF Expression in Neisseria Gonorrhoeae and Its Role in High-Level Antimicrobial Resistance. In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when gonococci are grown under inducing conditions. &amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329546</id>
		<title>Sandbox Reserved 386</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_386&amp;diff=1329546"/>
		<updated>2011-12-07T17:23:34Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pmq&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;MtrF General Structure pdb:3PMQ&#039; /&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;General Information&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF is a cell surface cytochrome on the Gram-negative bacteria known as &#039;&#039;Shewanella oneidensis&#039;&#039;. MtrF is involved with shuttling electrons across its (&#039;&#039;S. oneidensis&#039;&#039;) outer surface. MtrF has several homologues, MtrC and the protein OmcA. These three different proteins are thought to be replaceable with one another in deletion mutation experiments.&amp;lt;ref name=&amp;quot;mtrf&amp;quot;&amp;gt; PMID:11418600&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Function&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF can play various roles in intermediating electron transfer straight to electron sinks, catalyzing electron exchange or partaking in extracellular intercytochrome electron exchange. Certain bacterial species (&#039;&#039;S. oneidensis&#039;&#039;) have the ability to utilize the extracellular mineral forms of iron and manganese as electron acceptors. In order for &#039;&#039;S. oneidensis&#039;&#039; to use these minerals, decaheme cytochromes must be present, they are positioned on the bacteria&#039;s cell wall at the endpoint of the trans-outer-membrane electron repositioning units. This process requires three different proteins to move electrons across the cell membrane; the process ends in a decaheme cytochrome labeled MtrF, in &#039;&#039;S. oneidensis&#039;&#039;. &amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF Structure&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
MtrF contains a few common &amp;lt;scene name=&#039;Sandbox_Reserved_386/Elements/2&#039;&amp;gt;elements&amp;lt;/scene&amp;gt;; O,N,Fe and Ca, Oxygen is the most abundant element and is spread out through the entire protein, there are several Nitrogens that form rings that have an Iron placed in the center, there is also a lone Calcium ion. There are &amp;lt;scene name=&#039;Sandbox_Reserved_386/Alpha_beta/1&#039;&amp;gt;Alpha Helices and Beta sheets&amp;lt;/scene&amp;gt; positioned throughout MtrF, there are more alpha helices but they are randomly placed in the structure while there are fewer beta sheets and they are located on opposite ends from one another. MtrF as mentioned above is a decaheme cytochrome, which means that there are ten heme groups that are spatially organized throughout the protein. Each heme is spread about 7Å from its neighbor, this close space allows for speedy electron transfer. The (ten) hemes are organized across four domains in a distinctive cross conformation, a staggered 65-? Octaheme chain intersects the protein and is bisected by a planar 45-? Tetraheme chain. All of the hemes in the MtrF crystal structure display bis-His axial ligand coordination. The His residue in the domains provide the distal ligands for the five hemes in the same domain. Domains I and III contain antiparallel Beta-strands that connect two Greek key split Beta-barrel domains. Domains II and IV bind five closely packed hemes covalently attached Cys residues to the motifs in each domain. All the domains fold together so that the pentaheme domains II and IV are crowded together to form a central core with the two barrel domains I and III adjoining either side. The 3.2Å crystal structure proposes that the hemes, each corresponding to two His ligands, are near enough for effective electron transfer. Near-infrared magnetic circular dichroism and electron paramagnetic resonance spectroscopy provide additional support for these structural features. The complete structure of MtrF is similar to an ellipsoid with dimensions of 85x70x30Å. This particular structure was able to provide molecular insight into how the reduction of insoluble substrates, soluble substrates, and cytochrome redox partners may be possible together at different termini on an electron transport chain on the cell surface.&amp;lt;ref name=&amp;quot;mtrf&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;MtrF’s role in Diseases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;Neisseria gonorrhoeae&#039;&#039; is the bacteria that causes the STD Gonorrhea. This bacteria is quite resistant to many hydrophobic drugs, detergents, and dyes. The reason behind the tough resistance is the energy dependent efflux pump Mtr(Multiple transferable resistance).  MtrF has been identified as a cell envelope protein that is involved with the resistance of hydrophobic antimicrobials in &#039;&#039;Neisseria gonorrhoeae&#039;&#039;. MtrF is a protein that helps highlight the expression of detergent resistance by gonococci. MtrF is thought to act in accordance with the MtrC- MtrD- MtrE efflux pump; to make sure gonococci has high level resistance to specific hydrophobic agents. MtrF is located near the MtrR gene and is predicted to encode a cytoplasmic membrane protein that contains up to twelve transmembrane domains. The expression of MtrF is ultimately subject to MtrR’s transcriptional control. MtrF was given its name because it’s so closely tied to the protein MtrR. Several orthologues were discovered in a few Gram-negative and positive bacteria, indicating that perhaps the predicted products may represent an undescribed protein family that is highly involved with resistance of antimicrobials. &amp;lt;ref&amp;gt; PMID:12493784 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Regulation of MtrF&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
A prime example of MtrF regulation is the study of Regulation of mtrF Expression in Neisseria Gonorrhoeae and Its Role in High-Level Antimicrobial Resistance. In this study the expression of MtrF was repressed by MtrR (the major repressor in the mtrCDE expression). Another repressor known as MpeR can also regulate the expression of MtrF. Repression of MtrF by MtrR and MpeR was used, demonstrating that the repressive effects mediated by these regulators are independent processes. MtrF was also disabled and the significant reduction in the induction of hydrophobic agent resistance and it was found that the expression of MtrF is enhanced when gonococci are grown under inducing conditions. &amp;lt;ref&amp;gt; PMID:15901695 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1329542</id>
		<title>Sandbox Reserved 385</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1329542"/>
		<updated>2011-12-07T17:07:54Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&amp;lt;Structure load=&#039;3ert&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Estrogen Receptor Ligand-Binding Domain in Complex with 4-Hydroxytamoxifen&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Tamoxifen and Breast Cancer ==&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
Recent studies have shown that those with high estrogen levels, coupled with an already high risk of developing breast cancer, are at a higher risk of the disease occurring.&amp;lt;ref name=&amp;quot;danielle&amp;quot;&amp;gt;Skafar, D., and S. Koide. &amp;quot;Understanding the Human Estrogen Receptor-alpha Using Targeted Mutagenesis.&amp;quot; Molecular and Cellular Endocrinology 246.1-2 (2006): 83-90. &amp;lt;/ref&amp;gt; Estrogen is necessary in many areas of the body. It gives cells permission to grow, including cancer cells. Estrogen is regulated through an activated estrogen receptor transcription factor. These transcription factors in the higher risk patients can activate oncogenes that accelerate cancer cell growth. A recent hypothesis suggests that a new way to prevent and treat breast cancer is to change the way estrogen binds to the receptor. The drug Tamoxifen acts as a competitive inhibitor of estrogen and the estrogen receptor. Those with a higher risk of breast cancer who undergo treatment with Tamoxifen show low breast tissue density, which suggests a lower breast cancer risk. Tamoxifen is a smaller molecule that mimics the shape of estrogen, allowing it to bind tightly to the estrogen receptor. &lt;br /&gt;
&lt;br /&gt;
== Tamoxifen and the Estrogen Receptor ==&lt;br /&gt;
Tamoxifen lacks the second OH group as well as a tail containing oxygen and nitrogen on the ring.&amp;lt;ref name=&amp;quot;danielle&amp;quot; /&amp;gt; Tamoxifen binds to the ligand binging domain of the estrogen receptor, which leads to a conformational shift.&amp;lt;ref name=&amp;quot;danielle&amp;quot; /&amp;gt; The conformational change causes the &amp;lt;scene name=&#039;Sandbox_Reserved_385/12_helix_er/1&#039;&amp;gt;helix 12&amp;lt;/scene&amp;gt; to shift into an adjacent coactivator.&amp;lt;ref&amp;gt;Pecorak, Sara, and Tom Susman. &amp;quot;Tamoxifen, Diethylstilbesterol and the Estrogen Receptor Ligand Binding Region.&amp;quot; (04). Web. &amp;lt;http://biology.kenyon.edu/BMB/Chime2/2001/estrogen/FRAMES/start.htm&amp;gt;.&amp;lt;/ref&amp;gt; This site is essential for estrogen to do its job. Without the coactivator binding, the receptor remains inactive. Conformational changes also occur due to the new hydrophobic interactions between helices 3 and 11. These newly formed hydrophobic interactions lead to a cascade effect of conformational changes across the molecule. The new side chain also causes conformational changes since one of the rings in Tamoxifen is shoved deeper into the pocket. Tamoxifen also provides one less hydrogen bond in the pocket compared to estrogen, causing helices 3, 8, and 11 to extend. With the coactivator site blocked, there is a halt in proliferation, meaning that there is no cell growth.&lt;br /&gt;
== Tamoxifen, the Drug ==&lt;br /&gt;
Tamoxifen is a precursor for the drug that binds to the estrogen receptor, making it a prodrug. The actual drug is 4-hydroxyltamoxifen, which has a greater affinity for the estrogen receptor than Tamoxifen alone. The FDA approved this prodrug 30 years ago to prevent breast cancer in high risk patients. Tamoxifen is classfied as a Seletive Estrogen Receptor Modulator (SERM), meaning that it selectively blocks or activates the activity of estrogen on specific cells, such as breast cancer cells. While Tamoxifen is used to block estrogen acivity in breast cells, it also activates estrogen activity in other cells, such as bone and liver cells.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1329541</id>
		<title>Sandbox Reserved 385</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1329541"/>
		<updated>2011-12-07T17:04:09Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;3ert&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Estrogen Receptor Ligand-Binding Domain in Complex with 4-Hydroxytamoxifen&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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&lt;br /&gt;
== Tamoxifen and Breast Cancer ==&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
Recent studies have shown that those with high estrogen levels, coupled with an already high risk of developing breast cancer, are at a higher risk of the disease occurring.&amp;lt;ref name=&amp;quot;danielle&amp;quot;&amp;gt;Skafar, D., and S. Koide. &amp;quot;Understanding the Human Estrogen Receptor-alpha Using Targeted Mutagenesis.&amp;quot; Molecular and Cellular Endocrinology 246.1-2 (2006): 83-90. &amp;lt;/ref&amp;gt; Estrogen is necessary in many areas of the body. It gives cells permission to grow, including cancer cells. Estrogen is regulated through an activated estrogen receptor transcription factor. These transcription factors in the higher risk patients can activate oncogenes that accelerate cancer cell growth. A recent hypothesis suggests that a new way to prevent and treat breast cancer is to change the way estrogen binds to the receptor. The drug Tamoxifen acts as a competitive inhibitor of estrogen and the estrogen receptor. Those with a higher risk of breast cancer who undergo treatment with Tamoxifen show low breast tissue density, which suggests a lower breast cancer risk. Tamoxifen is a smaller molecule that mimics the shape of estrogen, allowing it to bind tightly to the estrogen receptor. &lt;br /&gt;
&lt;br /&gt;
== Tamoxifen and the Estrogen Receptor ==&lt;br /&gt;
Tamoxifen lacks the second OH group as well as a tail containing oxygen and nitrogen on the ring.&amp;lt;ref name=&amp;quot;danielle&amp;quot; /&amp;gt; Tamoxifen binds to the ligand binging domain of the estrogen, which leads to a conformational shift.&amp;lt;ref name=&amp;quot;danielle&amp;quot; /&amp;gt; The conformational change causes the &amp;lt;scene name=&#039;Sandbox_Reserved_385/12_helix_er/1&#039;&amp;gt;helix 12&amp;lt;/scene&amp;gt; to shift into an adjacent coactivator.&amp;lt;ref&amp;gt;Pecorak, Sara, and Tom Susman. &amp;quot;Tamoxifen, Diethylstilbesterol and the Estrogen Receptor Ligand Binding Region.&amp;quot; (04). Web. &amp;lt;http://biology.kenyon.edu/BMB/Chime2/2001/estrogen/FRAMES/start.htm&amp;gt;.&lt;br /&gt;
&amp;lt;/ref&amp;gt; This site is essential for estrogen to do its job. Without the coactivator binding, the receptor remains inactive. Conformational changes also occur due to the new hydrophobic interactions between helices 3 and 11. These newly formed hydrophobic interactions lead to a cascade effect of conformational changes across the molecule. The new side chain also causes conformational changes since one of the rings in Tamoxifen is shoved deeper into the pocket. Tamoxifen also provides one less hydrogen bond in the pocket compared to estrogen, causing helices 3, 8, and 11 to extend. With the coactivator site blocked, there is a halt in proliferation, meaning that there is no cell growth.&lt;br /&gt;
== Tamoxifen, the Drug ==&lt;br /&gt;
Tamoxifen is a precursor for the drug that binds to the estrogen receptor, making it a prodrug. The actual drug is 4-hydroxyltamoxifen, which has a greater affinity for the estrogen receptor than Tamoxifen alone. The FDA approved this prodrug 30 years ago to prevent breast cancer in high risk patients. Tamoxifen is classfied as a Seletive Estrogen Receptor Modulator (SERM), meaning that it selectively blocks or activates the activity of estrogen on specific cells, such as breast cancer cells. While Tamoxifen is used to block estrogen acivity in breast cells, it also activates estrogen activity in other cells, such as bone and liver cells.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1329540</id>
		<title>Sandbox Reserved 385</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1329540"/>
		<updated>2011-12-07T17:01:06Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
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&amp;lt;Structure load=&#039;3ert&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Estrogen Receptor Ligand-Binding Domain in Complex with 4-Hydroxytamoxifen&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Tamoxifen and Breast Cancer ==&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
Recent studies have shown that those with high estrogen levels, coupled with an already high risk of developing breast cancer, are at a higher risk of the disease occurring.&amp;lt;ref name=&amp;quot;danielle&amp;quot;&amp;gt;Skafar, D., and S. Koide. &amp;quot;Understanding the Human Estrogen Receptor-alpha Using Targeted Mutagenesis.&amp;quot; Molecular and Cellular Endocrinology 246.1-2 (2006): 83-90. &amp;lt;/ref&amp;gt; Estrogen is necessary in many areas of the body. Estrogen gives cells permission to grow, including cancer cells. Estrogen is regulated through an activated estrogen receptor transcription factor. These transcription factors in the higher risk patients can activate oncogenes that accelerate cancer cell growth. A new hypothesis suggests that a new way to prevent and treat breast cancer is to change the way estrogen binds to the receptor. The drug Tamoxifen acts as a competitive inhibitor of estrogen and the estrogen receptor. Those with a higher risk of breast cancer that undergo treatment with Tamoxifen show low breast tissue density, which suggests a lower breast cancer risk. Tamoxifen is a smaller molecule that mimics the shape of estrogen, allowing it to bind tightly to the estrogen receptor. &lt;br /&gt;
&lt;br /&gt;
== Tamoxifen and the Estrogen Receptor ==&lt;br /&gt;
Tamoxifen lacks the second OH group as well as a tail containing oxygen and nitrogen on the ring.&amp;lt;ref name=&amp;quot;danielle&amp;quot; /&amp;gt; Tamoxifen binds to the ligand binging domain of the estrogen, which leads to a conformational shift.&amp;lt;ref name=&amp;quot;danielle&amp;quot; /&amp;gt; The conformational change causes the &amp;lt;scene name=&#039;Sandbox_Reserved_385/12_helix_er/1&#039;&amp;gt;helix 12&amp;lt;/scene&amp;gt; to shift into an adjacent coactivator.&amp;lt;ref&amp;gt;Pecorak, Sara, and Tom Susman. &amp;quot;Tamoxifen, Diethylstilbesterol and the Estrogen Receptor Ligand Binding Region.&amp;quot; (04). Web. &amp;lt;http://biology.kenyon.edu/BMB/Chime2/2001/estrogen/FRAMES/start.htm&amp;gt;.&lt;br /&gt;
&amp;lt;/ref&amp;gt; This site is essential for estrogen to do its job. Without the coactivator binding, the receptor remains inactive. Conformational changes also occur due to the new hydrophobic interactions between helices 3 and 11. These newly formed hydrophobic interactions lead to a cascade effect of conformational changes across the molecule. The new side chain also causes conformational changes since one of the rings in Tamoxifen is shoved deeper into the pocket. Tamoxifen also provides one less hydrogen bond in the pocket compared to estrogen, causing helices 3, 8, and 11 to extend. With the coactivator site blocked, there is a halt in proliferation, meaning that there is no cell growth.&lt;br /&gt;
== Tamoxifen, the Drug ==&lt;br /&gt;
Tamoxifen is a precursor for the drug that binds to the estrogen receptor, making it a prodrug. The actual drug is 4-hydroxyltamoxifen, which has a greater affinity for the estrogen receptor than Tamoxifen alone. The FDA approved this prodrug 30 years ago to prevent breast cancer in high risk patients. Tamoxifen is classfied as a Seletive Estrogen Receptor Modulator (SERM), meaning that it selectively blocks or activates the activity of estrogen on specific cells, such as breast cancer cells. While Tamoxifen is used to block estrogen acivity in breast cells, it also activates estrogen activity in other cells, such as bone and liver cells.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1329538</id>
		<title>Sandbox Reserved 384</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1329538"/>
		<updated>2011-12-07T16:53:26Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;2qkh&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Glucose-dependant insulinotropic polypeptide receptor, [[2qkh]]&#039; scene=&#039;&#039; /&amp;gt;&lt;br /&gt;
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{{STRUCTURE_2qkh|  PDB=2qkh  | SIZE=400| SCENE= |right|CAPTION=Glucose-dependent insulinotropic polypeptide receptor, [[2qkh]] }}&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
=Glucose-dependent Insulinotropic Polypeptide Receptor=&lt;br /&gt;
==Background==&lt;br /&gt;
Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a transmembrane protein which is responsible for boosting glucose-induced insulin production. The transcription of this protein is positively controlled by glucose molecules; GIPR is expressed in higher levels when glucose is in higher concentration. The receptor is a multispan membrane-bound protein (shown in blue) consisting of an alpha helix, half twist helices, and beta sheets bound in several locations with disulfide bonds within itself. The ligand which binds to GIPR is glucose-dependent insulinotropic polypeptide (GIP), also known as gastric inhibitory polypeptide (shown in green). GIP is an alpha helical endogenous polypeptide hormone which is released upon the ingestion of food, specifically the carbohydrate glucose. &lt;br /&gt;
&lt;br /&gt;
===Molecular Function===&lt;br /&gt;
The purpose of the receptor is to bind glucose-dependent insulinotropic polypeptide (GIP) in the presence of glucose. This causes a chain reaction that increases secretion of insulin molecules. GIP binds to GIPR though &amp;lt;scene name=&#039;Sandbox_Reserved_384/Hydrophobics/1&#039;&amp;gt;hydrophobic interactions&amp;lt;/scene&amp;gt; and causes the release of G protein-coupled receptors, which in turn causes an enzymatic cascade resulting in the increased secretion of insulin. This occurs in the pancreatic islet beta-cells. It is likely that the cause of type 2 diabetes is due to the inability of GIP to bind properly to GIPR.&amp;lt;ref&amp;gt;PMID:11334402&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Ongoing Research===&lt;br /&gt;
The significance of this receptor makes it a prime target for diabetes research. Incretins are a class of biological molecules that act like gastrointestinal hormones. One such example is glucagon-like peptide-1 (GLP-1), which works with GIP to regulate the body&#039;s insulin levels. Synthetic versions of this peptide hormone have been made to treat people with type-2 diabetes. It works by stimulating GIP production as well as insulin secretion causing the body to properly regulate its blood glucose levels like someone without diabetes. The benefit of synthetic GLP-1 is that it is not protein and so would not be degraded as easily therefore prolonging the benefits of the drug. One such example is Byetta&amp;lt;ref&amp;gt;&amp;quot;Byetta.&amp;quot; BYETTA (exenatide) Injection | Welcome to BYETTA.com. Amylin Pharmaceuticals, Inc., 2011. Web. 02 Dec. 2011. &amp;lt;http://www.byetta.com/Pages/index.aspx&amp;gt;&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
[[Image:F3.large.jpg |400px| |left| |caption=&amp;lt;ref&amp;gt;&amp;quot;A Novel Pathway for Regulation of Glucose-dependent Insulinotropic Polypeptide (GIP) Receptor Expression in ß Cells.&amp;quot; The FASEB Journal 17.1 (2003): 91-93. Print.&amp;lt;/ref&amp;gt;|]]&lt;br /&gt;
{{Clear}}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===References=== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1329537</id>
		<title>Sandbox Reserved 384</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1329537"/>
		<updated>2011-12-07T16:52:36Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
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&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;2qkh&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Glucose-dependant insulinotropic polypeptide receptor, [[2qkh]]&#039; scene=&#039;&#039; /&amp;gt;&lt;br /&gt;
&amp;lt;!--&lt;br /&gt;
{{STRUCTURE_2qkh|  PDB=2qkh  | SIZE=400| SCENE= |right|CAPTION=Glucose-dependent insulinotropic polypeptide receptor, [[2qkh]] }}&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
=Glucose-dependent Insulinotropic Polypeptide Receptor=&lt;br /&gt;
==Background==&lt;br /&gt;
Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a transmembrane protein which is responsible for boosting glucose-induced insulin production. The transcription of this protein is positively controlled by glucose molecules; GIPR is expressed in higher levels when glucose is in higher concentration. The receptor is a multispan membrane-bound protein (shown in blue) consisting of an alpha helix, half twist helices, and beta sheets bound in several locations with disulfide bonds within itself. The ligand which binds to GIPR is glucose-dependent insulinotropic polypeptide (GIP), also known as gastric inhibitory polypeptide(shown in green). GIP is an alpha helical endogenous polypeptide hormone which is released upon the ingestion of food, specifically the carbohydrate glucose. &lt;br /&gt;
&lt;br /&gt;
===Molecular Function===&lt;br /&gt;
The purpose of the receptor is to bind glucose-dependent insulinotropic polypeptide (GIP) in the presence of glucose. This causes a chain reaction that increases secretion of insulin molecules. GIP binds to GIPR though &amp;lt;scene name=&#039;Sandbox_Reserved_384/Hydrophobics/1&#039;&amp;gt;hydrophobic interactions&amp;lt;/scene&amp;gt; and causes the release of G protein-coupled receptors, which in turn causes an enzymatic cascade resulting in the increased secretion of insulin. This occurs in the pancreatic islet beta-cells. It is likely that the cause of type 2 diabetes is due to the inability of GIP to bind properly to GIPR.&amp;lt;ref&amp;gt;PMID:11334402&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Ongoing Research===&lt;br /&gt;
The significance of this receptor makes it a prime target for diabetes research. Incretins are a class of biological molecules that act like gastrointestinal hormones. One such example is glucagon-like peptide-1 (GLP-1), which works with GIP to regulate the body&#039;s insulin levels. Synthetic versions of this peptide hormone have been made to treat people with type-2 diabetes. It works by stimulating GIP production as well as insulin secretion causing the body to properly regulate its blood glucose levels like someone without diabetes. The benefit of synthetic GLP-1 is that it is not protein and so would not be degraded as easily therefore prolonging the benefits of the drug. One such example is Byetta&amp;lt;ref&amp;gt;&amp;quot;Byetta.&amp;quot; BYETTA (exenatide) Injection | Welcome to BYETTA.com. Amylin Pharmaceuticals, Inc., 2011. Web. 02 Dec. 2011. &amp;lt;http://www.byetta.com/Pages/index.aspx&amp;gt;&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
[[Image:F3.large.jpg |400px| |left| |caption=&amp;lt;ref&amp;gt;&amp;quot;A Novel Pathway for Regulation of Glucose-dependent Insulinotropic Polypeptide (GIP) Receptor Expression in ß Cells.&amp;quot; The FASEB Journal 17.1 (2003): 91-93. Print.&amp;lt;/ref&amp;gt;|]]&lt;br /&gt;
{{Clear}}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===References=== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329532</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329532"/>
		<updated>2011-12-07T16:36:49Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&lt;br /&gt;
&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID:15148138&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID: 19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329531</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329531"/>
		<updated>2011-12-07T16:35:19Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID: 15148138&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID: 19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329530</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329530"/>
		<updated>2011-12-07T16:33:12Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID:15148138&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID:19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329529</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329529"/>
		<updated>2011-12-07T16:32:43Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID:15148138&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID:19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329528</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329528"/>
		<updated>2011-12-07T16:31:25Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID:15148138.&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID:19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329527</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329527"/>
		<updated>2011-12-07T16:30:36Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;PMID:15148138.&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;PMID:19520868&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;PMID:9473588&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329526</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329526"/>
		<updated>2011-12-07T16:17:38Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;Girault J, Greengard P (2004). &amp;quot;The neurobiology of dopamine signaling&amp;quot;. Arch Neurol 61 (5): 641–4. doi:10.1001/archneur.61.5.641. PMID 15148138.&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;&amp;quot;G protein-coupled receptor kinase 4 (GRK4) regulates the phosphorylation and function of the dopamine D3 receptor.&amp;quot;&lt;br /&gt;
Villar V.A.M., Jones J.E., Armando I., Palmes-Saloma C., Yu P., Pascua A.M., Keever L., Arnaldo F.B., Wang Z., Luo Y., Felder R.A., Jose P.A.&lt;br /&gt;
J. Biol. Chem. 284:21425-21434(2009) [PubMed: 19520868] [Abstract]&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;Suzuki M, Hurd YL, Sokoloff P, Schwartz JC, Sedvall G (January 1998). &amp;quot;D3 dopamine receptor mRNA is widely expressed in the human brain&amp;quot;. Brain Res. 779 (1–2): 58–74. doi:10.1016/S0006-8993(97)01078-0. PMID 9473588.&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329525</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329525"/>
		<updated>2011-12-07T16:15:45Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;Girault J, Greengard P (2004). &amp;quot;The neurobiology of dopamine signaling&amp;quot;. Arch Neurol 61 (5): 641–4. doi:10.1001/archneur.61.5.641. PMID 15148138.&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-protein coupled receptors are a family of transmembrane proteins that transmit chemical signals from outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-protein receptor&#039;s signaling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; The D3 receptor is located in the brain, suggesting that it plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is also contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;&amp;quot;G protein-coupled receptor kinase 4 (GRK4) regulates the phosphorylation and function of the dopamine D3 receptor.&amp;quot;&lt;br /&gt;
Villar V.A.M., Jones J.E., Armando I., Palmes-Saloma C., Yu P., Pascua A.M., Keever L., Arnaldo F.B., Wang Z., Luo Y., Felder R.A., Jose P.A.&lt;br /&gt;
J. Biol. Chem. 284:21425-21434(2009) [PubMed: 19520868] [Abstract]&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues, and the beta sheets are made up of 9 residues. The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons, and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;Suzuki M, Hurd YL, Sokoloff P, Schwartz JC, Sedvall G (January 1998). &amp;quot;D3 dopamine receptor mRNA is widely expressed in the human brain&amp;quot;. Brain Res. 779 (1–2): 58–74. doi:10.1016/S0006-8993(97)01078-0. PMID 9473588.&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors, which helps to diminish complications that are caused by certain diseases. Some agonists, agents that stimulate dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors, include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with the dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
&lt;br /&gt;
Lucotte G., Lagarde J.-P., Funalot B., Sokoloff P.&lt;br /&gt;
Clin. Genet. 69:437-440(2006) [PubMed: 16650084] [Abstract]&amp;lt;/ref&amp;gt;&amp;lt;ref&amp;gt;&amp;quot;A functional variant of the dopamine D3 receptor is associated with risk and age-at-onset of essential tremor.&amp;quot;&lt;br /&gt;
Jeanneteau F., Funalot B., Jankovic J., Deng H., Lagarde J.-P., Lucotte G., Sokoloff P.&lt;br /&gt;
Proc. Natl. Acad. Sci. U.S.A. 103:10753-10758(2006) [PubMed: 16809426] [Abstract]&amp;lt;/ref&amp;gt; Disorders that are linked to variations in the DRD3 gene include social phobia&amp;lt;ref&amp;gt;Schneier FR, Liebowitz MR, Abi-Dargham A, Zea-Ponce Y, Lin SH, Laruelle M (2000). &amp;quot;Low dopamine D(2) receptor binding potential in social phobia&amp;quot;. Am J Psychiatry 157 (3): 457–459. doi:10.1176/appi.ajp.157.3.457. PMID 10698826.&amp;lt;/ref&amp;gt;, Tourette’s syndrome&amp;lt;ref&amp;gt;11Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557.&amp;lt;/ref&amp;gt;, Parkinson’s disease&amp;lt;ref&amp;gt;Fuxe K, Manger P, Genedani S, Agnati L (2006). The nigrostriatal DA pathway and Parkinson’s disease. &amp;quot;The nigrostriatal DA pathway and Parkinson&#039;s disease&amp;quot;. J Neural Transm Suppl. Journal of Neural Transmission. Supplementa 70 (70): 71–83. doi:10.1007/978-3-211-45295-0_13. ISBN 978-3-211-28927-3. PMID 17017512.&amp;lt;/ref&amp;gt;, schizophrenia&amp;lt;ref&amp;gt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557.&amp;lt;/ref&amp;gt;, neuroleptic malignant syndrome&amp;lt;ref&amp;gt;Mihara K, Kondo T, Suzuki A, et al. (2003). &amp;quot;Relationship between functional dopamine D2 and D3 receptors gene polymorphisms and neuroleptic malignant syndrome&amp;quot;. Am. J. Med. Genet. B Neuropsychiatr. Genet. 117 (1): 57–60. doi:10.1002/ajmg.b.10025. PMID 12555236.&amp;lt;/ref&amp;gt;, attention-deficit hyperactivinty disorder (ADHD)&amp;lt;ref&amp;gt;Faraone S, Khan S (2006). &amp;quot;Candidate gene studies of attention-deficit/hyperactivity disorder&amp;quot;. J Clin Psychiatry 67 Suppl 8: 13–20. PMID 16961425.&amp;lt;/ref&amp;gt;, and drug and alcohol dependence&amp;lt;ref&amp;gt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557.&amp;lt;/ref&amp;gt; &amp;lt;ref&amp;gt;Hummel M, Unterwald E (2002). &amp;quot;D1 dopamine receptor: a putative neurochemical and behavioral link to cocaine action&amp;quot;. J Cell Physiol 191 (1): 17–27. doi:10.1002/jcp.10078. PMID 11920678&amp;lt;/ref&amp;gt;.&lt;br /&gt;
==References==&lt;br /&gt;
#&amp;lt;Girault J, Greengard P (2004). &amp;quot;The neurobiology of dopamine signaling&amp;quot;. Arch Neurol 61 (5): 641–4. doi:10.1001/archneur.61.5.641. PMID 15148138./&amp;gt;&lt;br /&gt;
#&amp;lt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20./&amp;gt;&lt;br /&gt;
#&amp;lt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5./&amp;gt;&lt;br /&gt;
#&amp;lt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011./&amp;gt;&lt;br /&gt;
#&amp;lt;&amp;quot;G protein-coupled receptor kinase 4 (GRK4) regulates the phosphorylation and function of the dopamine D3 receptor.&amp;quot; Villar V.A.M., Jones J.E., Armando I., Palmes-Saloma C., Yu P., Pascua A.M., Keever L., Arnaldo F.B., Wang Z., Luo Y., Felder R.A., Jose P.A. J. Biol. Chem. 284:21425-21434(2009) [PubMed: 19520868] [Abstract]/&amp;gt;&lt;br /&gt;
#&amp;lt;http://www.pdb.org/pdb/explore.do?structureId=3PBL/&amp;gt;&lt;br /&gt;
#&amp;lt;Suzuki M, Hurd YL, Sokoloff P, Schwartz JC, Sedvall G (January 1998). &amp;quot;D3 dopamine receptor mRNA is widely expressed in the human brain&amp;quot;. Brain Res. 779 (1–2): 58–74. doi:10.1016/S0006-8993(97)01078-0. PMID 9473588./&amp;gt;&lt;br /&gt;
#&amp;lt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists/&amp;gt;&lt;br /&gt;
#&amp;lt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists/&amp;gt;&lt;br /&gt;
#&amp;lt;http://www.pdb.org/pdb/explore.do?structureId=3PBL/&amp;gt;&lt;br /&gt;
#&amp;lt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot; Lucotte G., Lagarde J.-P., Funalot B., Sokoloff P. Clin. Genet. 69:437-440(2006) [PubMed: 16650084] [Abstract]/&amp;gt;&lt;br /&gt;
#&amp;lt;&amp;quot;A functional variant of the dopamine D3 receptor is associated with risk and age-at-onset of essential tremor.&amp;quot; Jeanneteau F., Funalot B., Jankovic J., Deng H., Lagarde J.-P., Lucotte G., Sokoloff P. Proc. Natl. Acad. Sci. U.S.A. 103:10753-10758(2006) [PubMed: 16809426] [Abstract]/&amp;gt;&lt;br /&gt;
#&amp;lt;Schneier FR, Liebowitz MR, Abi-Dargham A, Zea-Ponce Y, Lin SH, Laruelle M (2000). &amp;quot;Low dopamine D(2) receptor binding potential in social phobia&amp;quot;. Am J Psychiatry 157 (3): 457–459. doi:10.1176/appi.ajp.157.3.457. PMID 10698826./&amp;gt;&lt;br /&gt;
#&amp;lt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557./&amp;gt;&lt;br /&gt;
#&amp;lt;Fuxe K, Manger P, Genedani S, Agnati L (2006). The nigrostriatal DA pathway and Parkinson’s disease. &amp;quot;The nigrostriatal DA pathway and Parkinson&#039;s disease&amp;quot;. J Neural Transm Suppl. Journal of Neural Transmission. Supplementa 70 (70): 71–83. doi:10.1007/978-3-211-45295-0_13. ISBN 978-3-211-28927-3. PMID 17017512./&amp;gt;&lt;br /&gt;
#&amp;lt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557./&amp;gt;&lt;br /&gt;
#&amp;lt;Mihara K, Kondo T, Suzuki A, et al. (2003). &amp;quot;Relationship between functional dopamine D2 and D3 receptors gene polymorphisms and neuroleptic malignant syndrome&amp;quot;. Am. J. Med. Genet. B Neuropsychiatr. Genet. 117 (1): 57–60. doi:10.1002/ajmg.b.10025. PMID 12555236./&amp;gt;&lt;br /&gt;
#&amp;lt;Faraone S, Khan S (2006). &amp;quot;Candidate gene studies of attention-deficit/hyperactivity disorder&amp;quot;. J Clin Psychiatry 67 Suppl 8: 13–20. PMID 16961425./&amp;gt;&lt;br /&gt;
#&amp;lt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557./&amp;gt;&lt;br /&gt;
#&amp;lt;Hummel M, Unterwald E (2002). &amp;quot;D1 dopamine receptor: a putative neurochemical and behavioral link to cocaine action&amp;quot;. J Cell Physiol 191 (1): 17–27. doi:10.1002/jcp.10078. PMID 11920678/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329523</id>
		<title>Sandbox Reserved 383</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_383&amp;diff=1329523"/>
		<updated>2011-12-07T15:54:25Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Human Dopamine D3 Receptor==&lt;br /&gt;
&amp;lt;Structure load=&#039;3PBL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Structure of the human dopamine D3 receptor in complex with eticlopride&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
==Introduction==&lt;br /&gt;
Dopamine receptors are a class of metabotropic G protein-coupled receptors that are important in the central nervous system. Dopamine receptors are involved in many neurological processes that comprise motivation, pleasure, cognition, memory, learning, and fine motor skills. There are five subtype dopamine receptors, D1, D2, D3, D4, and D5. The D3 receptor is a part of the D2-like family.&amp;lt;ref&amp;gt;Girault J, Greengard P (2004). &amp;quot;The neurobiology of dopamine signaling&amp;quot;. Arch Neurol 61 (5): 641–4. doi:10.1001/archneur.61.5.641. PMID 15148138.&amp;lt;/ref&amp;gt; &lt;br /&gt;
==Function==&lt;br /&gt;
Human dopamine D3 receptor is a protein that is encoded by the dopamine receptor gene (DRD3).&amp;lt;ref&amp;gt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20.&amp;lt;/ref&amp;gt; The DRD3 gene codes for the D3 dopamine receptor that inhibits adenylyl cyclase through inhibitory G-proteins. G-proteins are a family of transmembrane proteins that transmit chemical signals outside the cell to cause changes inside of the cell. Adenylate cyclase is part of the G-proteins signalling and catalyze the conversion of ATP to cyclic AMP (cAMP).&amp;lt;ref&amp;gt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.&amp;lt;/ref&amp;gt; This receptor is located in the brain, suggesting that the D3 receptor plays a role in cognitive and emotional functions.&amp;lt;ref&amp;gt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011.&amp;lt;/ref&amp;gt; The human dopamine D3 receptor is membrane-bound and scattered in the cytoplasm. Receptor stimulation causes internalization of the receptors at the perinuclear areas. This is followed by the spreading of the receptors to the membrane. DRD3 is contained in lipid rafts of renal proximal tubule cells.&amp;lt;ref&amp;gt;&amp;quot;G protein-coupled receptor kinase 4 (GRK4) regulates the phosphorylation and function of the dopamine D3 receptor.&amp;quot;&lt;br /&gt;
Villar V.A.M., Jones J.E., Armando I., Palmes-Saloma C., Yu P., Pascua A.M., Keever L., Arnaldo F.B., Wang Z., Luo Y., Felder R.A., Jose P.A.&lt;br /&gt;
J. Biol. Chem. 284:21425-21434(2009) [PubMed: 19520868] [Abstract]&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Structure==&lt;br /&gt;
Human dopamine D3 receptor is 64% helical and 1% beta sheet. The protein is composed of 20 helices and 3 beta sheet strands. The helices are made up of 312 residues and the bate sheets are made up of 9 residues.  The entire protein consists of 481 residues.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt; Dopamine D3 receptors are greatly expressed in the Islands of Calleja, a group of neural granule cells located within the ventral striatum in the brains of most animals, which is part of the limbic system. It is also found in the nucleus accumbens, a collection of neurons and forms the main part of the ventral striatum.&amp;lt;ref&amp;gt;Suzuki M, Hurd YL, Sokoloff P, Schwartz JC, Sedvall G (January 1998). &amp;quot;D3 dopamine receptor mRNA is widely expressed in the human brain&amp;quot;. Brain Res. 779 (1–2): 58–74. doi:10.1016/S0006-8993(97)01078-0. PMID 9473588.&amp;lt;/ref&amp;gt;&lt;br /&gt;
 [[Image:250px-Islands_of_Calleja_Rat.jpg|250px|left|thumb| Islands of Calleja of rat brain stained in blue.]]&lt;br /&gt;
[[Image:250PX-~2.JPG|250px|left|thumb| Nucleus accumbens visible in red.]]&lt;br /&gt;
&lt;br /&gt;
==Ligands==&lt;br /&gt;
Many non-selective prescription drugs bind to the D3 receptor. The binding of drugs either increases or inhibits the production of dopamine D3 receptors which helps to diminish complications that are caused by certain diseases. Some agonist, agents that stimulate, dopamine receptors include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Amphetamine&lt;br /&gt;
*Dopaminergic&lt;br /&gt;
*Methamphetamine&lt;br /&gt;
Some antagonists, agents that inhibit dopamine receptors include&amp;lt;ref&amp;gt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists&amp;lt;/ref&amp;gt;:&lt;br /&gt;
*Bromopride&lt;br /&gt;
*Clebopride&lt;br /&gt;
*Eticlopride&lt;br /&gt;
*Nafadotride&lt;br /&gt;
Two ligands that are associated with dopamine D3 receptor are 3-chloro-5-ethyl-N{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxyl-2-methyloxybenzamide (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Etq/1&#039;&amp;gt;ETQ&amp;lt;/scene&amp;gt;) and maltose (&amp;lt;scene name=&#039;Sandbox_Reserved_383/Mal/1&#039;&amp;gt;MAL&amp;lt;/scene&amp;gt;).  ETQ binds to dopamine D3 receptor by Asp 110A and Phe346A. MAL binds by Asp 1020A, Glu 1022A, Glu1011A, and Leu1032A.&amp;lt;ref&amp;gt;http://www.pdb.org/pdb/explore.do?structureId=3PBL&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Diseases==&lt;br /&gt;
Variations in the DRD3 gene is connected with essential tremor hereditary type 1 (ETM1). ETM1 is the most common movement disorder involving postural tremor of the arms, head, legs, body core, voice, jaw, and other facial muscles. This condition can be provoked by emotions, hunger, fatigue, and temperature extremes.&amp;lt;ref&amp;gt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot;&lt;br /&gt;
Lucotte G., Lagarde J.-P., Funalot B., Sokoloff P.&lt;br /&gt;
Clin. Genet. 69:437-440(2006) [PubMed: 16650084] [Abstract]&amp;lt;/ref&amp;gt;&amp;lt;ref&amp;gt;&amp;quot;A functional variant of the dopamine D3 receptor is associated with risk and age-at-onset of essential tremor.&amp;quot;&lt;br /&gt;
Jeanneteau F., Funalot B., Jankovic J., Deng H., Lagarde J.-P., Lucotte G., Sokoloff P.&lt;br /&gt;
Proc. Natl. Acad. Sci. U.S.A. 103:10753-10758(2006) [PubMed: 16809426] [Abstract]&amp;lt;/ref&amp;gt; Disorders that are linked to variations in the DRD3 gene include social phobia&amp;lt;ref&amp;gt;Schneier FR, Liebowitz MR, Abi-Dargham A, Zea-Ponce Y, Lin SH, Laruelle M (2000). &amp;quot;Low dopamine D(2) receptor binding potential in social phobia&amp;quot;. Am J Psychiatry 157 (3): 457–459. doi:10.1176/appi.ajp.157.3.457. PMID 10698826.&amp;lt;/ref&amp;gt;, Tourette’s syndrome&amp;lt;ref&amp;gt;11Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557.&amp;lt;/ref&amp;gt;, Parkinson’s disease&amp;lt;ref&amp;gt;Fuxe K, Manger P, Genedani S, Agnati L (2006). The nigrostriatal DA pathway and Parkinson’s disease. &amp;quot;The nigrostriatal DA pathway and Parkinson&#039;s disease&amp;quot;. J Neural Transm Suppl. Journal of Neural Transmission. Supplementa 70 (70): 71–83. doi:10.1007/978-3-211-45295-0_13. ISBN 978-3-211-28927-3. PMID 17017512.&amp;lt;/ref&amp;gt;, schizophrenia&amp;lt;ref&amp;gt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557.&amp;lt;/ref&amp;gt;, neuroleptic malignant syndrome&amp;lt;ref&amp;gt;Mihara K, Kondo T, Suzuki A, et al. (2003). &amp;quot;Relationship between functional dopamine D2 and D3 receptors gene polymorphisms and neuroleptic malignant syndrome&amp;quot;. Am. J. Med. Genet. B Neuropsychiatr. Genet. 117 (1): 57–60. doi:10.1002/ajmg.b.10025. PMID 12555236.&amp;lt;/ref&amp;gt;, attention-deficit hyperactivinty disorder (ADHD)&amp;lt;ref&amp;gt;Faraone S, Khan S (2006). &amp;quot;Candidate gene studies of attention-deficit/hyperactivity disorder&amp;quot;. J Clin Psychiatry 67 Suppl 8: 13–20. PMID 16961425.&amp;lt;/ref&amp;gt;, and drug and alcohol dependence&amp;lt;ref&amp;gt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557.&amp;lt;/ref&amp;gt; &amp;lt;ref&amp;gt;Hummel M, Unterwald E (2002). &amp;quot;D1 dopamine receptor: a putative neurochemical and behavioral link to cocaine action&amp;quot;. J Cell Physiol 191 (1): 17–27. doi:10.1002/jcp.10078. PMID 11920678&amp;lt;/ref&amp;gt;.&lt;br /&gt;
==References==&lt;br /&gt;
#&amp;lt;Girault J, Greengard P (2004). &amp;quot;The neurobiology of dopamine signaling&amp;quot;. Arch Neurol 61 (5): 641–4. doi:10.1001/archneur.61.5.641. PMID 15148138./&amp;gt;&lt;br /&gt;
#&amp;lt;Le Coniat M, Sokoloff P, Hillion J, Martres MP, Giros B, Pilon C, Schwartz JC, Berger R (Oct 1991). &amp;quot;Chromosomal localization of the human D3 dopamine receptor gene&amp;quot;. Hum Genet 87 (5): 618–20./&amp;gt;&lt;br /&gt;
#&amp;lt;Reece, Jane; Campbell, Neil (2002). Biology. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5./&amp;gt;&lt;br /&gt;
#&amp;lt;National Center for Biotechnology Information, U.S. National Library of Medicine. DRD3 dopamine receptor D3 [Homo sapiens]. 19 November 2011./&amp;gt;&lt;br /&gt;
#&amp;lt;&amp;quot;G protein-coupled receptor kinase 4 (GRK4) regulates the phosphorylation and function of the dopamine D3 receptor.&amp;quot; Villar V.A.M., Jones J.E., Armando I., Palmes-Saloma C., Yu P., Pascua A.M., Keever L., Arnaldo F.B., Wang Z., Luo Y., Felder R.A., Jose P.A. J. Biol. Chem. 284:21425-21434(2009) [PubMed: 19520868] [Abstract]/&amp;gt;&lt;br /&gt;
#&amp;lt;http://www.pdb.org/pdb/explore.do?structureId=3PBL/&amp;gt;&lt;br /&gt;
#&amp;lt;Suzuki M, Hurd YL, Sokoloff P, Schwartz JC, Sedvall G (January 1998). &amp;quot;D3 dopamine receptor mRNA is widely expressed in the human brain&amp;quot;. Brain Res. 779 (1–2): 58–74. doi:10.1016/S0006-8993(97)01078-0. PMID 9473588./&amp;gt;&lt;br /&gt;
#&amp;lt;http://en.wikipedia.org/wiki/Category:Dopamine_agonists/&amp;gt;&lt;br /&gt;
#&amp;lt;http://en.wikipedia.org/wiki/Category:Dopamine_antagonists/&amp;gt;&lt;br /&gt;
#&amp;lt;http://www.pdb.org/pdb/explore.do?structureId=3PBL/&amp;gt;&lt;br /&gt;
#&amp;lt;&amp;quot;Linkage with the Ser9Gly DRD3 polymorphism in essential tremor families.&amp;quot; Lucotte G., Lagarde J.-P., Funalot B., Sokoloff P. Clin. Genet. 69:437-440(2006) [PubMed: 16650084] [Abstract]/&amp;gt;&lt;br /&gt;
#&amp;lt;&amp;quot;A functional variant of the dopamine D3 receptor is associated with risk and age-at-onset of essential tremor.&amp;quot; Jeanneteau F., Funalot B., Jankovic J., Deng H., Lagarde J.-P., Lucotte G., Sokoloff P. Proc. Natl. Acad. Sci. U.S.A. 103:10753-10758(2006) [PubMed: 16809426] [Abstract]/&amp;gt;&lt;br /&gt;
#&amp;lt;Schneier FR, Liebowitz MR, Abi-Dargham A, Zea-Ponce Y, Lin SH, Laruelle M (2000). &amp;quot;Low dopamine D(2) receptor binding potential in social phobia&amp;quot;. Am J Psychiatry 157 (3): 457–459. doi:10.1176/appi.ajp.157.3.457. PMID 10698826./&amp;gt;&lt;br /&gt;
#&amp;lt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557./&amp;gt;&lt;br /&gt;
#&amp;lt;Fuxe K, Manger P, Genedani S, Agnati L (2006). The nigrostriatal DA pathway and Parkinson’s disease. &amp;quot;The nigrostriatal DA pathway and Parkinson&#039;s disease&amp;quot;. J Neural Transm Suppl. Journal of Neural Transmission. Supplementa 70 (70): 71–83. doi:10.1007/978-3-211-45295-0_13. ISBN 978-3-211-28927-3. PMID 17017512./&amp;gt;&lt;br /&gt;
#&amp;lt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557./&amp;gt;&lt;br /&gt;
#&amp;lt;Mihara K, Kondo T, Suzuki A, et al. (2003). &amp;quot;Relationship between functional dopamine D2 and D3 receptors gene polymorphisms and neuroleptic malignant syndrome&amp;quot;. Am. J. Med. Genet. B Neuropsychiatr. Genet. 117 (1): 57–60. doi:10.1002/ajmg.b.10025. PMID 12555236./&amp;gt;&lt;br /&gt;
#&amp;lt;Faraone S, Khan S (2006). &amp;quot;Candidate gene studies of attention-deficit/hyperactivity disorder&amp;quot;. J Clin Psychiatry 67 Suppl 8: 13–20. PMID 16961425./&amp;gt;&lt;br /&gt;
#&amp;lt;Kienast T, Heinz A (2006). &amp;quot;Dopamine and the diseased brain&amp;quot;. CNS Neurol Disord Drug Targets 5 (1): 109–31. doi:10.2174/187152706784111560. PMID 16613557./&amp;gt;&lt;br /&gt;
#&amp;lt;Hummel M, Unterwald E (2002). &amp;quot;D1 dopamine receptor: a putative neurochemical and behavioral link to cocaine action&amp;quot;. J Cell Physiol 191 (1): 17–27. doi:10.1002/jcp.10078. PMID 11920678/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_382&amp;diff=1329504</id>
		<title>Sandbox Reserved 382</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_382&amp;diff=1329504"/>
		<updated>2011-12-07T15:10:21Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
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&lt;br /&gt;
&lt;br /&gt;
= Aromatase =&lt;br /&gt;
&amp;lt;Structure load=&#039;3EQM&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Crystal structure of human placental aromatase cytochrome P450 in complex with androstenedione (PDB entry [http://www.pdb.org/pdb/explore/explore.do?structureId=3EQM])&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
Aromatase belongs to the cytochrome P450 family (CYP). During aromatization reactions, aromatase forms an electron-transfer complex with its partner, NADPH-cytochrome P450 reductase. This enzyme is localized in the endoplasmic reticulum of the cell, and tissue specific promoters regulate its activity.&amp;lt;ref&amp;gt; PMID:21125383 &amp;lt;/ref&amp;gt; In a number of species, including humans, aromatase can be found throughout the body in places such as the brain, gonads, blood vessels, endometrium, skin, bone and tissues including the placenta and adipose tissue.&amp;lt;ref&amp;gt;  PMID: 11427156 &amp;lt;/ref&amp;gt; &lt;br /&gt;
== Function ==&lt;br /&gt;
The primary function of aromatase is to produce estrogens by aromatizing androgens. Aromatase is the only known enzyme in vertebrates capable of catalyzing the aromatization of a six-membered ring&amp;lt;ref name=&amp;quot;structure&amp;quot;&amp;gt; Ghosh, D., Griswold, J., Erman, M., Pangborn, W. &amp;quot; X-ray Structure of Human Aromatase Reveals An Androgen-Specific Active Site&amp;quot; [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826573/]&amp;lt;/ref&amp;gt;. Aromatase converts androstenedione to estrogen and testosterone to estradiol.&amp;lt;ref name=&amp;quot;products&amp;quot; /&amp;gt; Aromatase is also a key enzyme in the biosynthesis of estrogens through a process called steroidogenesis. This enzyme helps produce the female sex hormone, estrogen, that helps to fuel the growth of hormone receptor-positive breast cancer. &lt;br /&gt;
There are many environmental factors that affect the activity of the aromatase enzyme and disrupt its function. Factors that increase the activity of the enzyme include age, obesity, gonadotropins, insulin, anti-m llerian hormone, alcohol and smoking.&amp;lt;ref name=&amp;quot;products&amp;quot;&amp;gt; &amp;quot;Aromatase Products&amp;quot; [http://www.novusbio.com/aromatase#13225047480835&amp;amp;ga_enabled%3B0] &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[Image:Aromatase_Structure.jpg|thumb|260px|left| Ribbon diagram displaying the overall structure of human placental aromatase. &amp;lt;ref name=&amp;quot;structure&amp;quot;/&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Structure==&lt;br /&gt;
Due to the membrane-bound nature of mammalian CYP enzymes, the structural characterization is extremely difficult. Aromatase is a monomeric enzyme composed of a heme-prosthetic group and a single polypeptide chain consisting of 503 amino acid residues.&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt; One important feature of CYPs is the iron-containing &amp;lt;scene name=&#039;Sandbox_Reserved_382/Porphyrin/1&#039;&amp;gt;porphyrin&amp;lt;/scene&amp;gt; group at the enzyme active site.&amp;lt;ref&amp;gt; PMID: 16395678 &amp;lt;/ref&amp;gt; The &amp;lt;scene name=&#039;Sandbox_Reserved_382/Heme_iron/3&#039;&amp;gt;heme iron&amp;lt;/scene&amp;gt; is within the porphyrin and is considered the reaction center of the enzyme. The &amp;lt;scene name=&#039;Sandbox_Reserved_382/Ligand/3&#039;&amp;gt;ligand&amp;lt;/scene&amp;gt; docks in a region adjacent to the porphyrin. Aromatase is anchored to the endoplasmic reticulum by the amino terminal transmembrane domain. The tertiary structure of aromatase includes twelve major α-helices and ten β-strands.&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt; An androstenedione molecule is bound in the active site of the enzyme. The active site of the enzyme can be found in the distal cavity of the heme-binding pocket. &#039;&#039;&#039;A ribbon diagram displaying the overall structure of the human placental aromatase is shown to the left.&#039;&#039;&#039; The amino terminus starts at residue 45 and is shown in dark blue. The carboxyl terminus ending at residue 496 is shown in red. The helices are labeled A-L and the sheets are labeled 1-10 accordingly. The heme group and the bound ligand are shown in the center of the protein. &amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Aromatase Inhibitors ==&lt;br /&gt;
Inhibitors of aromatase stop estrogen production in post-menopausal women. This action is done by blocking the aromatase enzyme by turning the hormone, androgen, into small amounts of estrogen.&amp;lt;ref&amp;gt; &amp;quot;Aromatase Inhibitors&amp;quot; [http://www.breastcancer.org/treatment/hormonal/aromatase_inhibitors/] &amp;lt;/ref&amp;gt;&lt;br /&gt;
There are three aromatase inhibitors that are often used in the treatment of breast cancer:&lt;br /&gt;
*Arimidex (Anastrozole)&lt;br /&gt;
*Aromasin (Exemestane)&lt;br /&gt;
*Femara (Letrozole)&lt;br /&gt;
Aromatase inhibitors are unable to stop ovaries from producing estrogen; therefore, these inhibitors only work in post-menopausal women. &lt;br /&gt;
== Disorders ==&lt;br /&gt;
*&#039;&#039;&#039;Aromatase Enzyme Deficiency&#039;&#039;&#039;&lt;br /&gt;
Aromatase deficiency is rare in humans; however, if aromatase is nonfunctional due to a mutation, estrogen synthesis cannot occur. Affected females are diagnosed at birth because of the obvious characteristics of pseudohermaphroditism. During the childhood of these girls, delayed bone maturation can occur along with cystic ovaries. However, affected males are diagnosed later in life because there are not obvious birth defects. Clincal symptoms such as a tall physique, delayed bone maturation, epiphyseal closure, bone pain, and excess adiposy.&amp;lt;ref&amp;gt; PMID: 17452968 &amp;lt;/ref&amp;gt;&lt;br /&gt;
*&#039;&#039;&#039;Aromatase Excess Syndrome&#039;&#039;&#039;&lt;br /&gt;
Research shows a rare disorder caused by excessive aromatase activity that can cause familial gynecomastia and feminization of both sexes. This can be inherited in an autosomal dominant manner, affecting females and males differently. Females with this disorder showed signs of isosexual precocity and/or macromastia. Males showed characteristics of heterosexual precocity and/or gynecomastia.&amp;lt;ref&amp;gt; PMID: 9543166 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_381&amp;diff=1327664</id>
		<title>Sandbox Reserved 381</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_381&amp;diff=1327664"/>
		<updated>2011-12-06T18:12:52Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pe3&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Ternary complex O-GlcNAc transferase with UDP&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== O-GlcNAc transferase ==&lt;br /&gt;
&lt;br /&gt;
O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase) is an essential mammalian enzyme that acts as a nutrient sensor, coupling metabolic status to the regulation of a wide variety of cellular signaling pathways.&amp;lt;ref&amp;gt; Hart GW, Housley MP, Slawson C. Cycling of O-linked β-N-acetylglucosamine on nucleocytoplasmic proteins. Nature.2007;446:1017-22.[http://www.nature.com/nature/journal/v446/n7139/abs/nature05815.html]&amp;lt;/ref&amp;gt; OGT catalyses the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to serines and threonines of cytoplasmic, nuclear and mitochondrial proteins, including numerous transcription factors, tumour suppressors, kinases, phospahateses and histone-modifying proteins.&amp;lt;ref&amp;gt;PMID:21240259&amp;lt;/ref&amp;gt; Two crystal structures of human OGT are reported here as a ternary complex with UDP and a &amp;lt;scene name=&#039;Sandbox_Reserved_381/Binary_complex_with_udp/1&#039;&amp;gt;binary complex&amp;lt;/scene&amp;gt; with UDP and a peptide substrate.&lt;br /&gt;
&lt;br /&gt;
== O-GlcNAc transferase Function ==&lt;br /&gt;
The major mechanism for nutrient sensing in eukaryotes involves OGT. OGT senses cellular glucose levels via UDP-GlcNAc concentration, and responds by O-GlcNAcylating a broad range of nuclear anf cytoplasmic proteins.&amp;lt;ref&amp;gt;PMID:17460662&amp;lt;/ref&amp;gt; Insulin-like signaling pathways and transcriptional activators that regulate glucose levels by controlling gluconeogenisis include proteins that are O-GlcNAcylated by OGT.&amp;lt;ref&amp;gt;PMID:18288188&amp;lt;/ref&amp;gt; Numerous O-GlcNAcylation sites are also phosphorylation sites. OGT is suggested to play a major role in modulating cellular kinase signaling cascades.&amp;lt;ref&amp;gt;PMID:12269319&amp;lt;/ref&amp;gt; Widespread transcriptional regulations also involve OGT.&amp;lt;ref&amp;gt;PMID:19478141&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Modifications ==&lt;br /&gt;
O-GlcNAc modification has been described for a large and still increasing number of proteins, many of which are key modulators of cellular signalling. O-GlcNAc modifications are catalysed by a OGT, and are removed by the antagonistic enzyme β-N-acetylglucosaminidase (O-GlcNAcase). The general scheme of O-linked N-acetylglucosamine modification suggests that N-acetylglucosamine is added to serine/threonine (Ser/Thr) residues of target proteins by the enzyme OGT, using UDP-GlcNAc as substrate. The N-acetylglucosamine group is removed by the antagonistic activity of O-GlcNAcase.&amp;lt;ref&amp;gt;Alexander G, Danilo G. The O-linked N-acetylglucosamine modification in cellular signalling and the immune system. EMBO reports. 2008 June;9:748-753[http://www.nature.com/embor/journal/v9/n8/full/embor2008129.html]&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Features of Interest ==&lt;br /&gt;
The OGT protein possess two ligands &amp;lt;scene name=&#039;Sandbox_Reserved_381/So4_ligand/1&#039;&amp;gt;SO4&amp;lt;/scene&amp;gt; and uridine-5-diphosphate &amp;lt;scene name=&#039;Sandbox_Reserved_381/Udp/1&#039;&amp;gt;(UDP)&amp;lt;/scene&amp;gt;. OGT is the only known member to glycosylate polypeptides, and it contains a long uncharacterized intervening sequence (~120 amino acids) in the middle of the catalytic region. Studies suggest that OGT contains a phosphatidylinositol (3,4,5)-trisphosphate (PIP&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)binding domain. The most unusual feature of OGT is the intervening domain between the catalytic lobes, which is only found in metazoans.  This polypeptide adopts a topologically novel fold with a seven-stranded &amp;lt;scene name=&#039;Sandbox_Reserved_381/Ogt_structure/1&#039;&amp;gt;beta sheet&amp;lt;/scene&amp;gt; core stabilized by flanking alpha helices. There are two long &amp;lt;scene name=&#039;Sandbox_Reserved_381/Unstructured_loops/1&#039;&amp;gt;unstructured loops&amp;lt;/scene&amp;gt; for which electron density is missing.&amp;lt;ref&amp;gt; PMID:18288188&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Structure ==&lt;br /&gt;
OGT is comprised of two distinct regions: a multidomain catalytic region, which has no available structure and an N-terminal region consisting of a series of tetratricopeptide repeat(TPR) units.&amp;lt;ref&amp;gt;PMID:9083067&amp;lt;/ref&amp;gt; The N terminus of OGT is unusual, consisting of 2.5-13.5 tetratricopeptide repeats (TPRs) depending on alternative splicing.&amp;lt;ref&amp;gt;Kreppel L, Hart G. Regulation of a cytosolic and nuclear O-GlcNAc transferase. Role of the tetratricopeptide repeats. J Biol Chem. 1999;274:32015-32022&amp;lt;/ref&amp;gt; The N-terminal domain of tetratricopeptide (TPR) mediates the recognition of a broad range of target proteins. Components of the nuclear pore complex are major OGT targets, as OGT depletion by RNA interference (RNAi) results in the loss of GlcNAc modification at the nuclear envelope.   &lt;br /&gt;
&lt;br /&gt;
== N Terminus ==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;1W3B&#039; size=&#039;250&#039; side=&#039;left&#039; caption=&#039;Superhelical TPR domain of OGT, structural similarities to importin alpha. (PDB entry [[1W3B]])&#039; scene=&#039;&#039;&amp;gt;The crystal structure of the homodimeric TPR domain of human OGT, which contains 11.5 TPR repeats gives insight into the mechanism of target recognition.  The repeats form an elongated superhilix. The concave surface of the superhelix is lined by absolutely conserved asparagines, in a manner reminiscent of the peptide-binding site of importin alpha. Based on this structural similarity, it is proposed that OGT uses an analogous molecular mechanism to recognize its targets.&amp;lt;ref&amp;gt;PMID:15361863&amp;lt;/ref&amp;gt; &amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Mediated Disease ==&lt;br /&gt;
Faulty regulation of O-GlcNAc midifications has been suggested to be involved in neurodegenerative diseases, diabetes mellitus and cancer. Biochemical details of these processes are still unclear.&amp;lt;ref&amp;gt;PMID:16051707&amp;lt;/ref&amp;gt; Proteins modified by O-GlcNAc have been directly shown to have a role in the pathology of human diseases. For instance, the Ser/The kinase AKT,PI&amp;lt;sub&amp;gt;(3)&amp;lt;/sub&amp;gt;K,insulin receptor substrate 1, glycogen synthase and endothelial nitric oxide synthase,all of which are enzymes that have a crucial role in insulin signalling,are reversibly modified by OGT. A recent study showed that recruitment of OGT to the plasma membrane specifically prevents the phosphorylation of AKT and possibly other proteins, thereby terminating insulin signalling.&amp;lt;ref&amp;gt;PMID:18288188&amp;lt;/ref&amp;gt; This adds evidence to the view that increasing the level of O-GlcNAc modifications correlates with the development of insulin resistance, which is a characteristic of type II diabetes.&amp;lt;ref&amp;gt;PMID:16317114&amp;lt;/ref&amp;gt;&amp;lt;ref&amp;gt;PMID:16781888&amp;lt;/ref&amp;gt; Some indications suggest that O-GlcNAc modifications have a role in Alzheimer disease. Higher levels of O-GlcNAc can be detected in the brain tissue, and several proteins involved in neuronal signaling are modified with O-GlcNAc. Among them are the β-amyloid precursor protein, clathrin-assembly proteins and neurofilaments. In the brains of patients with Alzheimer disease, hyperphosphorylated Tau protein was modified by O-GlcNAc to a lesser extent than in healthy individuals.&amp;lt;ref&amp;gt;PMID:17940659&amp;lt;/ref&amp;gt; Studies have shown that some oncogenes and tumour suppressors are targets of O-glycosylation, including the SV40 T antigen and c-MYC.&amp;lt;ref&amp;gt;PMID:14533811&amp;lt;/ref&amp;gt; Tumour cells have an altered glucose metabolism that is expected to produce changes in O-GlcNAc levels and to affect different signaling pathways.&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_381&amp;diff=1327661</id>
		<title>Sandbox Reserved 381</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_381&amp;diff=1327661"/>
		<updated>2011-12-06T15:36:22Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3pe3&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Ternary complex O-GlcNAc transferase with UDP&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;O-GlcNAc transferase&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase) is an essential mammalian enzyme that acts as a nutrient sensor, coupling metabolic status to the regulation of a wide variety of cellular signaling pathways.&amp;lt;ref&amp;gt; Hart GW, Housley MP, Slawson C. Cycling of O-linked β-N-acetylglucosamine on nucleocytoplasmic proteins. Nature.2007;446:1017-22.[http://www.nature.com/nature/journal/v446/n7139/abs/nature05815.html]&amp;lt;/ref&amp;gt; OGT catalyses the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to serines and threonines of cytoplasmic, nuclear and mitochondrial proteins, including numerous transcription factors, tumour suppressors, kinases, phospahateses and histone-modifying proteins.&amp;lt;ref&amp;gt;PMID:21240259&amp;lt;/ref&amp;gt; Two crystal structures of human OGT are reported here as a ternary complex with UDP and a &amp;lt;scene name=&#039;Sandbox_Reserved_381/Binary_complex_with_udp/1&#039;&amp;gt;binary complex&amp;lt;/scene&amp;gt; with UDP and a peptide substrate.&lt;br /&gt;
&lt;br /&gt;
== O-GlcNAc transferase Function ==&lt;br /&gt;
The major mechanism for nutrient sensing in eukaryotes involves OGT. OGT senses cellular glucose levels via UDP-GlcNAc concentration, and responds by O-GlcNAcylating a broad range of nuclear anf cytoplasmic proteins.&amp;lt;ref&amp;gt;PMID:17460662&amp;lt;/ref&amp;gt; Insulin-like signaling pathways and transcriptional activators that regulate glucose levels by controlling gluconeogenisis include proteins that are O-GlcNAcylated by OGT.&amp;lt;ref&amp;gt;PMID:18288188&amp;lt;/ref&amp;gt; Numerous O-GlcNAcylation sites are also phosphorylation sites. OGT is suggested to play a major role in modulating cellular kinase signaling cascades.&amp;lt;ref&amp;gt;PMID:12269319&amp;lt;/ref&amp;gt; Widespread transcriptional regulations also involve OGT.&amp;lt;ref&amp;gt;PMID:19478141&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Modifications ==&lt;br /&gt;
O-GlcNAc modification has been described for a large and still increasing number of proteins, many of which are key modulators of cellular signalling. O-GlcNAc modifications are catalysed by a OGT, and are removed by the antagonistic enzyme β-N-acetylglucosaminidase (O-GlcNAcase). The general scheme of O-linked N-acetylglucosamine modification suggests that N-acetylglucosamine is added to serine/threonine (Ser/Thr) residues of target proteins by the enzyme OGT, using UDP-GlcNAc as substrate. The N-acetylglucosamine group is removed by the antagonistic activity of O-GlcNAcase.&amp;lt;ref&amp;gt;Alexander G, Danilo G. The O-linked N-acetylglucosamine modification in cellular signalling and the immune system. EMBO reports. 2008 June;9:748-753[http://www.nature.com/embor/journal/v9/n8/full/embor2008129.html]&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Features of Interest ==&lt;br /&gt;
The OGT protein possess two ligands &amp;lt;scene name=&#039;Sandbox_Reserved_381/So4_ligand/1&#039;&amp;gt;SO4&amp;lt;/scene&amp;gt; and uridine-5-diphosphate &amp;lt;scene name=&#039;Sandbox_Reserved_381/Udp/1&#039;&amp;gt;(UDP)&amp;lt;/scene&amp;gt;. OGT is the only known member to glycosylate polypeptides, and it contains a long uncharacterized intervening sequence (~120 amino acids) in the middle of the catalytic region. Studies suggest that OGT contains a phosphatidylinositol (3,4,5)-trisphosphate (PIP&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)binding domain. The most unusual feature of OGT is the intervening domain between the catalytic lobes, which is only found in metazoans.  This polypeptide adopts a topologically novel fold with a seven-stranded &amp;lt;scene name=&#039;Sandbox_Reserved_381/Ogt_structure/1&#039;&amp;gt;beta sheet&amp;lt;/scene&amp;gt; core stabilized by flanking alpha helices. There are two long &amp;lt;scene name=&#039;Sandbox_Reserved_381/Unstructured_loops/1&#039;&amp;gt;unstructured loops&amp;lt;/scene&amp;gt; for which electron density is missing.&amp;lt;ref&amp;gt; PMID:18288188&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Structure ==&lt;br /&gt;
OGT is comprised of two distinct regions: a multidomain catalytic region, which has no available structure and an N-terminal region consisting of a series of tetratricopeptide repeat(TPR) units.&amp;lt;ref&amp;gt;PMID:9083067&amp;lt;/ref&amp;gt; The N terminus of OGT is unusual, consisting of 2.5-13.5 tetratricopeptide repeats (TPRs) depending on alternative splicing.&amp;lt;ref&amp;gt;Kreppel L, Hart G. Regulation of a cytosolic and nuclear O-GlcNAc transferase. Role of the tetratricopeptide repeats. J Biol Chem. 1999;274:32015-32022&amp;lt;/ref&amp;gt; The N-terminal domain of tetratricopeptide (TPR) mediates the recognition of a broad range of target proteins. Components of the nuclear pore complex are major OGT targets, as OGT depletion by RNA interference (RNAi) results in the loss of GlcNAc modification at the nuclear envelope.   &lt;br /&gt;
&lt;br /&gt;
== N Terminus ==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;1W3B&#039; size=&#039;250&#039; side=&#039;left&#039; caption=&#039;Superhelical TPR domain of OGT, structural similarities to importin alpha. (PDB entry [[1W3B]])&#039; scene=&#039;&#039;&amp;gt;The crystal structure of the homodimeric TPR domain of human OGT, which contains 11.5 TPR repeats gives insight into the mechanism of target recognition.  The repeats form an elongated superhilix. The concave surface of the superhelix is lined by absolutely conserved asparagines, in a manner reminiscent of the peptide-binding site of importin alpha. Based on this structural similarity, it is proposed that OGT uses an analogous molecular mechanism to recognize its targets.&amp;lt;ref&amp;gt;PMID:15361863&amp;lt;/ref&amp;gt; &amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== OGT Mediated Disease ==&lt;br /&gt;
Faulty regulation of O-GlcNAc midifications has been suggested to be involved in neurodegenerative diseases, diabetes mellitus and cancer. Biochemical details of these processes are still unclear.&amp;lt;ref&amp;gt;PMID:16051707&amp;lt;/ref&amp;gt; Proteins modified by O-GlcNAc have been directly shown to have a role in the pathology of human diseases. For instance, the Ser/The kinase AKT,PI&amp;lt;sub&amp;gt;(3)&amp;lt;/sub&amp;gt;K,insulin receptor substrate 1, glycogen synthase and endothelial nitric oxide synthase,all of which are enzymes that have a crucial role in insulin signalling,are reversibly modified by OGT. A recent study showed that recruitment of OGT to the plasma membrane specifically prevents the phosphorylation of AKT and possibly other proteins, thereby terminating insulin signalling.&amp;lt;ref&amp;gt;PMID:18288188&amp;lt;/ref&amp;gt; This adds evidence to the view that increasing the level of O-GlcNAc modifications correlates with the development of insulin resistance, which is a characteristic of type II diabetes.&amp;lt;ref&amp;gt;PMID:16317114&amp;lt;/ref&amp;gt;&amp;lt;ref&amp;gt;PMID:16781888&amp;lt;/ref&amp;gt; Some indications suggest that O-GlcNAc modifications have a role in Alzheimer disease. Higher levels of O-GlcNAc can be detected in the brain tissue, and several proteins involved in neuronal signaling are modified with O-GlcNAc. Among them are the β-amyloid precursor protein, clathrin-assembly proteins and neurofilaments. In the brains of patients with Alzheimer disease, hyperphosphorylated Tau protein was modified by O-GlcNAc to a lesser extent than in healthy individuals.&amp;lt;ref&amp;gt;PMID:17940659&amp;lt;/ref&amp;gt; Studies have shown that some oncogenes and tumour suppressors are targets of O-glycosylation, including the SV40 T antigen and c-MYC.&amp;lt;ref&amp;gt;PMID:14533811&amp;lt;/ref&amp;gt; Tumour cells have an altered glucose metabolism that is expected to produce changes in O-GlcNAc levels and to affect different signaling pathways.&lt;br /&gt;
&lt;br /&gt;
==References== &lt;br /&gt;
&lt;br /&gt;
&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1327556</id>
		<title>Sandbox Reserved 387</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1327556"/>
		<updated>2011-12-02T21:17:36Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3RJ1&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;Mediator&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
== Mediator ==&lt;br /&gt;
&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
== Mediator Structure ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_387/Head_module/1&#039;&amp;gt;head module&amp;lt;/scene&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Regulation Mechanism ==&lt;br /&gt;
&lt;br /&gt;
Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell.  Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold.  This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression.  In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.&lt;br /&gt;
In Bacillus subtilis, the 5&#039;-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. &amp;lt;ref&amp;gt;PMID: 15610857 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1327551</id>
		<title>Sandbox Reserved 387</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_387&amp;diff=1327551"/>
		<updated>2011-12-02T20:57:10Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_JMeans}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3RJ1&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;left&#039; caption=&#039;Mediator&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
== Mediator ==&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_402/Initial_structure_with_bases/2&#039;&amp;gt;guanine riboswitch&amp;lt;/scene&amp;gt; .&amp;lt;ref&amp;gt;PMID: 15610857 &amp;lt;/ref&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
== Mediator Structure ==&lt;br /&gt;
 &amp;lt;scene name=&#039;Sandbox_Reserved_387/Binding_site/2&#039;&amp;gt;ligand&amp;lt;/scene&amp;gt;   &amp;lt;ref&amp;gt;PMID: 17175531 &amp;lt;/ref&amp;gt;&lt;br /&gt;
  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Regulation Mechanism ==&lt;br /&gt;
&lt;br /&gt;
Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell.  Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold.  This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression.  In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.&lt;br /&gt;
In Bacillus subtilis, the 5&#039;-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. &amp;lt;ref&amp;gt;PMID: 15610857 &amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1327546</id>
		<title>Sandbox Reserved 384</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_384&amp;diff=1327546"/>
		<updated>2011-12-02T20:28:27Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;2qkh&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Glucose-dependant insulinotropic polypeptide receptor, [[2qkh]]&#039; scene=&#039;&#039; /&amp;gt;&lt;br /&gt;
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{{STRUCTURE_2qkh|  PDB=2qkh  | SIZE=400| SCENE= |right|CAPTION=Glucose-dependent insulinotropic polypeptide receptor, [[2qkh]] }}&lt;br /&gt;
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=Glucose-dependent Insulinotropic Polypeptide Receptor=&lt;br /&gt;
==Background==&lt;br /&gt;
Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a transmembrane protein which is responsible for boosting glucose-induced insulin production. The transcription of this protein is positively controlled by glucose molecules, GIPR is expressed in higher levels when glucose is in higher concentration. The receptor is a multispan membrane bound protein (shown in blue) consisting of an alpha helix, half twist helices, and beta sheets binded in several locations with disulfide bonds within itself. The ligand which binds  to GIPR is Glucose-dependent insulinotropic polypeptide (GIP) also known as Gastric inhibitory polypeptide(shown in green). GIP is an alpha helical endogenous polypeptide hormone which is released upon the ingestion of food, specifically the carbohydrate glucose. &lt;br /&gt;
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===Molecular Function=== &lt;br /&gt;
The purpose of the receptor is to bind Glucose-dependent insulinotropic polypeptide (GIP) in the presence of Glucose. This causes a chain reaction that increases secretion of insulin molecules. GIP binds to GIPR though &amp;lt;scene name=&#039;Sandbox_Reserved_384/Hydrophobics/1&#039;&amp;gt;hydrophobic interactions&amp;lt;/scene&amp;gt; and causes the release of G protein-coupled receptors which in turn causes an enzymatic cascade resulting in the increased secretion of insulin. This occurs in the pancreatic islet beta-cells. It is likely that the cause of type 2 diabetes is due to the inability of GIP to bind properly to GIPR.&amp;lt;ref&amp;gt;PMID:11334402&amp;lt;/ref&amp;gt;&lt;br /&gt;
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===Ongoing Research===&lt;br /&gt;
The significance of this receptor makes it a prime target for diabetes research.  &lt;br /&gt;
[[Image:F3.large.jpg |400px| |left|]]&lt;br /&gt;
{{Clear}}&lt;br /&gt;
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===References=== &lt;br /&gt;
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&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1327498</id>
		<title>Sandbox Reserved 385</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_385&amp;diff=1327498"/>
		<updated>2011-12-01T22:08:08Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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&amp;lt;Structure load=&#039;3ert&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Estrogen Receptor Ligand-Binding Domain in Complex with 4-Hydroxytamoxifen&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
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&amp;lt;ref&amp;gt; Bizzini B. Tetanus Toxin. Microbiological Reviews.1979 June;43(2):224-236.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC281472/pdf/microrev00006-0112.pdf?tool=pmcentrez]&amp;lt;/ref&amp;gt;&lt;br /&gt;
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&amp;lt;ref&amp;gt;PMID:11807088&amp;lt;/ref&amp;gt;&lt;br /&gt;
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== Tamoxifen and Breast Cancer ==&lt;br /&gt;
&#039;&#039;&#039;&lt;br /&gt;
Recent studies have shown that those with high estrogen levels, coupled with an already high risk of developing breast cancer are at a higher risk of the disease occurring. Estrogen is necessary in many areas of the body. Estrogen gives cells permission to grow, including cancer cells. Estrogen is regulated through an activated estrogen receptor transcription factor. These transcription factors in the higher risk patients can activate oncogenes that accelerate cancer cell growth. A new hypothesis suggests that a new way to prevent and treat breast cancer is to change the way estrogen binds to the receptor. The drug Tamoxifen acts as a competitive inhibitor of estrogen and the estrogen receptor. Those with a higher risk of breast cancer that undergo treatment with Tamoxifen show low breast tissue density, which suggests a lower breast cancer risk. Tamoxifen is a smaller molecule that mimics the shape of estrogen, allowing it to bind tightly to the estrogen receptor. &lt;br /&gt;
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== Tamoxifen and the Estrogen Receptor ==&lt;br /&gt;
Tamoxifen lacks the second OH group as well as a tail containing oxygen and nitrogen on the ring. Tamoxifen binds to the ligand binging domain of the estrogen, which leads to a conformational shift. The conformational change causes the helix 12 to shift into an adjacent coactivator. This site is essential for estrogen to do its job. Without the coactivator binding, the receptor remains inactive. Conformational changes also occur due to the new hydrophobic interactions between helices 3 and 11. These newly formed hydrophobic interactions lead to a cascade effect of conformational changes across the molecule. The new side chain also causes conformational changes since one of the rings in Tamoxifen is shoved deeper into the pocket. Tamoxifen also provides one less hydrogen bond in the pocket compared to estrogen, causing &amp;lt;scene name=&#039;Sandbox_Reserved_385/Test_scene/1&#039;&amp;gt;helices 3, 8, and 11&amp;lt;/scene&amp;gt; to extend. With the coactivator site blocked, there is a hault in proliferation, meaning that there is no cell growth.&lt;br /&gt;
== Tamoxifen, the Drug ==&lt;br /&gt;
Tamoxifen is a precursor for the drug that binds to the estrogen receptor, making it a prodrug. The actual drug is 4-hydroxyltamoxifen, which has a greater affinity for the estrogen receptor than Tamoxifen alone. The FDA approved this prodrug 30 years ago to prevent breast cancer in high risk patients. Tamoxifen is classfied as a Seletive Estrogen Receptor Modulator (SERM), meaning that it selectively blocks or activates the activity of estrogen on specific cells, such as breast cancer cells. While Tamoxifen is used to block estrogen acivity in breast cells, it also activates estrogen actrivity in other cells, such as bone and liver cells.&lt;br /&gt;
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[[Image:estrogen.PNG|The Drug Tamoxifen and the Tamoxifen-Estrogen Complex. The green area represents the change in signal loop due to conformational changes after ligand-binding of Tamoixfen.]]&lt;br /&gt;
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==References== &lt;br /&gt;
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&amp;lt;references /&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_382&amp;diff=1327495</id>
		<title>Sandbox Reserved 382</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_382&amp;diff=1327495"/>
		<updated>2011-12-01T21:38:17Z</updated>

		<summary type="html">&lt;p&gt;John Means: &lt;/p&gt;
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= Aromatase =&lt;br /&gt;
&amp;lt;Structure load=&#039;3EQM&#039; size=&#039;400&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Crystal structure of human placental aromatase cytochrome P450 in complex with androstenedione (PDB entry [http://www.pdb.org/pdb/explore/explore.do?structureId=3EQM])&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
Aromatase belongs to the cytochrome p450 family. During aromatization reactions, Aromatase forms an electron-transfer complex with its partner, NADPH-cytochrome p450 reductase. This enzyme is localized in the endoplasmic reticulum of the cell and tissue specific promoters regulate its activity. &amp;lt;ref&amp;gt; PMID:21125383 &amp;lt;/ref&amp;gt; In a number of species, including humans, aromatase can be found throughout the body in places such as the brain, gonads, blood vessels, endometrium, skin, bone and tissues including the placenta and adipose tissue. &amp;lt;ref&amp;gt;  PMID: 11427156 &amp;lt;/ref&amp;gt; There are many environmental factors that affect the activity of the aromatase enzyme and disrupt its function. Factors that increase the activity of the enzyme include age, obesity, gonadotropins, insulin, anti-m llerian hormone, alcohol and smoking. &amp;lt;ref name=&amp;quot;products&amp;quot;&amp;gt; &amp;quot;Aromatase Products&amp;quot; [http://www.novusbio.com/aromatase#13225047480835&amp;amp;ga_enabled%3B0] &amp;lt;/ref&amp;gt;&lt;br /&gt;
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== Function ==&lt;br /&gt;
The primary function of Aromatase is to produce estrogens by aromatizing androgens. Aromatase is the only known enzyme in vertebrates capable of catalyzing the aromatization of a six-membered ring &amp;lt;ref name=&amp;quot;structure&amp;quot;&amp;gt; Ghosh, D., Griswold, J., Erman, M., Pangborn, W. &amp;quot; X-ray Structure of Human Aromatase Reveals An Androgen-Specific Active Site&amp;quot; [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826573/]&amp;lt;/ref&amp;gt;. Aromatase converts androstenedione to estrogen and testosterone to estradiol. &amp;lt;ref name=&amp;quot;products&amp;quot; /&amp;gt; Aromatase is also a key enzyme in the biosynthesis of estrogens through a process called steroidogenesis. This enzyme helps produce this female sex hormone, estrogen, that helps to fuel the growth of hormone receptor-positive breast cancer.&lt;br /&gt;
[[Image:Aromatase_Structure.jpg|thumb|260px|left| Ribbon diagram displaying the overall structure of human placental aromatase. &amp;lt;ref name=&amp;quot;structure&amp;quot;/&amp;gt;]]&lt;br /&gt;
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== Structure==&lt;br /&gt;
Due to the membrane-bound nature of mammalian cytochromes P450 (CYP), the structural characterization is extremely difficult. Aromatase is a monomeric enzyme composed of a heme-prosthetic group and a single polypeptide chain consisting of 503 amino-acid residues. &amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt; One important feature of CYPs is the iron-containing porphyrin group at the enzyme active site. &amp;lt;ref&amp;gt; PMID: 16395678 &amp;lt;/ref&amp;gt; Aromatase is anchored to the endoplasmic reticulum by the amino terminal transmembrane domain. The tertiary structure of Aromatase includes twelve major α-helices and ten β-strands&amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt;. An androstenedione molecule is bound to the active site of the enzyme. The active site of the enzyme can be found in the distal cavity of the heme-binding pocket. The &amp;lt;scene name=&#039;Sandbox_Reserved_382/Heme_iron/3&#039;&amp;gt;heme iron&amp;lt;/scene&amp;gt; is within the porphyrin and is considered the reaction center of the enzyme. The &amp;lt;scene name=&#039;Sandbox_Reserved_382/Ligand/2&#039;&amp;gt;ligand&amp;lt;/scene&amp;gt; is the region attached to the the porphyrin.&lt;br /&gt;
&#039;&#039;&#039;A ribbon diagram displaying the overall structure of the human placental aromatase is shown to the left.&#039;&#039;&#039; The amino terminus starts at residue 45 and is shown in dark blue. The carboxyl terminus ending at residue 496 is shown in red. The helices are labeled A-L and the sheets are labeled 1-10 accordingly. The heme group and the bound ligand are shown in the center of the protein. &amp;lt;ref name=&amp;quot;structure&amp;quot; /&amp;gt;&lt;br /&gt;
== Aromatase Inhibitors ==&lt;br /&gt;
Inhibitors of Aromatase stop the estrogen production in post-menopausal women. This action is done by blocking the Aromatase enzyme by turning the hormone, androgen, into small amounts of estrogen. &amp;lt;ref&amp;gt; &amp;quot;Aromatase Inhibitors&amp;quot; [http://www.breastcancer.org/treatment/hormonal/aromatase_inhibitors/] &amp;lt;/ref&amp;gt;&lt;br /&gt;
There are three Aromatase Inhibitors that are often used in the treatment of breast cancer:&lt;br /&gt;
*Arimidex (Anastrozole)&lt;br /&gt;
*Aromasin (Exemestane)&lt;br /&gt;
*Femara (Letrozole)&lt;br /&gt;
Aromatase Inhibitors are unable to stop ovaries from producing estrogen, therefore, these inhibitors only work in post-menopausal women. &lt;br /&gt;
== Disorders ==&lt;br /&gt;
*&#039;&#039;&#039;Aromatase Enzyme Deficiency&#039;&#039;&#039;&lt;br /&gt;
Aromatase Dificiency is rare in humans, however, if aromatase is nonfunctional due to a mutation estrogen synthesis cannot occur. Affected females are diagnoses at birth because of the obvious characteristics of pseudohermaphroditism. During the childhood of these girls, delayed bone maturation can occur along with cystic ovaries. However, affected males are diagnosed later in life because there are not obvious birth defects. Clincal symptoms such as a tall physique, delayed bone maturation and epiphyseal closure, bone pain, and excess adiposy. &amp;lt;ref&amp;gt; PMID: 17452968 &amp;lt;/ref&amp;gt;&lt;br /&gt;
*&#039;&#039;&#039;Aromatase Excess Syndrome&#039;&#039;&#039;&lt;br /&gt;
Research shows a rare disorder caused by excessive aromatase activity that can cause familial gynecomastia and feminization of both sexes. This can be inherited by an autosomal dominant manner, affected females and males differently. Females with this disorder showed signs of isosexual precocity and/or macromastia. Males showed characteristics of heterosexual precocity and/or gynecomastia. &amp;lt;ref&amp;gt; PMID: 9543166 &amp;lt;/ref&amp;gt;&lt;br /&gt;
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== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>John Means</name></author>
	</entry>
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