https://proteopedia.org/index.php?action=history&feed=atom&title=Phillips_Academy_Computer-Aided_Protein_Visualization_LabPhillips Academy Computer-Aided Protein Visualization Lab - Revision history2026-09-15T00:13:45ZRevision history for this page on the wikiMediaWiki 1.43.8https://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947167&oldid=prevJeremiah C Hagler at 20:20, 15 September 20182018-09-15T20:20:16Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For all of the protein structures you will visualize below, once you click on the green link, the structure will appear in the structure window on the right side of the page. In the structure window, click on "Popup" button to open a larger popup window of this structure. You can toggle the spin of the structure on or off by clicking on the "Spin" button. Clicking and holding on the structure in the window will allow you to manipulate the structure, rotating in three-dimension.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For all of the protein structures you will visualize below, once you click on the green link, the structure will appear in the structure window on the right side of the page. In the structure window, click on "Popup" button to open a larger popup window of this structure. You can toggle the spin of the structure on or off by clicking on the "Spin" button. Clicking and holding on the structure in the window will allow you to manipulate the structure, rotating in three-dimension.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>On the right side of this window you will our first example of a protein represented in three dimensions. This is protein G from the Streptococcal bacterium....a small and very simple polypeptide that binds to antibodies and messes up their organization such that their ability to further activate an immune response is hampered. <del style="font-weight: bold; text-decoration: none;">As you can see in this cartoon representation of protein G, there are two main sub-structures (secondary structure) of this protein. In red is the alpha helix, while a beta sheet is in gold. The regions linking the alpha helix and beta sheets together are called turns or linking regions and are not considered to be discrete secondary structures since they are not tightly structured and tend to be floppy.</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>On the right side of this window you will our first example of a protein represented in three dimensions. This is protein G from the Streptococcal bacterium....a small and very simple polypeptide that binds to antibodies and messes up their organization such that their ability to further activate an immune response is hampered. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>1.Alpha helix <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene> Here you can see the alpha helix of protein G in red and in ball and stick representation. The beta sheet is gold, in cartoon representation. Now<scene name='79/795987/Pg/7'>click to view alpha helix in isolation</scene>. Here the alpha helix is completely isolated. The rest of the protein is hidden. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the primary sequence) is shown in red. The '''amino acid side chains''' are shown in tan (each type of amino acid has its own unique side chain, one of 20 different types). <del style="font-weight: bold; text-decoration: none;">If a section of a protein's primary sequence of amino acids forms this coiled structure, it is known as an alpha-helix. </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">''Secondary Structure'': As you can see in this cartoon representation of protein G, there are two main sub-structures (secondary structure) of this protein. In red is the alpha helix, while a beta sheet is in gold. The regions linking the alpha helix and beta sheets together are called turns or linking regions (in white) and are not considered to be discrete secondary structures since they are not tightly structured and tend to be floppy.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>1.Alpha helix <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene> Here you can see the alpha helix of protein G in red and in ball and stick representation. The beta sheet is gold, in cartoon representation. Now <scene name='79/795987/Pg/7'>click to view alpha helix in isolation</scene>. Here the alpha helix is completely isolated. The rest of the protein is hidden. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the primary sequence) is shown in red. The '''amino acid side chains''' are shown in tan (each type of amino acid has its own unique side chain, one of 20 different types). </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2.Beta sheet <scene name='<del style="font-weight: bold; text-decoration: none;">71</del>/<del style="font-weight: bold; text-decoration: none;">713432</del>/<del style="font-weight: bold; text-decoration: none;">Protein_secondary_structure_bs</del>/<del style="font-weight: bold; text-decoration: none;">2</del>'>Click to see beta sheet</scene><scene name='79/795987/Pg/8'><del style="font-weight: bold; text-decoration: none;">Click </del>to see beta sheet in isolation</scene></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2.Beta sheet <scene name='<ins style="font-weight: bold; text-decoration: none;">79</ins>/<ins style="font-weight: bold; text-decoration: none;">795987</ins>/<ins style="font-weight: bold; text-decoration: none;">Pg</ins>/<ins style="font-weight: bold; text-decoration: none;">4</ins>'>Click to see <ins style="font-weight: bold; text-decoration: none;">the </ins>beta sheet <ins style="font-weight: bold; text-decoration: none;">in relation to the alpha helix</ins></scene> <ins style="font-weight: bold; text-decoration: none;">Here you can see the beta sheet of protein G gold, ball and stick representation. The alpha helix is red and in cartoon representation. Now </ins><scene name='79/795987/Pg/8'><ins style="font-weight: bold; text-decoration: none;">click </ins>to see beta sheet in isolation</scene><ins style="font-weight: bold; text-decoration: none;">. Here it the beta sheet is completely isolated. The rest of the protein is hidden. The amino acid backbone is in gold, the side chains in light blue.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> The second step of protein folding results in the '''tertiary structure''' (or 3° structure). Tertiary structure gives the protein an overall three-dimensional structure. The tertiary structure of a protein is determined by a combination of factors including hydrogen bonds, '''ionic bonds''' (between positively and negatively charged amino acids), '''covalent''' '''disulfide bonds''' (between cysteine residues), and '''Van der Waals''' interactions. Tertiary structure can also be affected by repulsive forces between similarly charged amino acids, as well as '''hydrophobic''' and '''hydrophilic''' interactions with a solvent (commonly water). At a distance many proteins form what look to be large globs at this point, and it is only upon more careful and close up inspection that one can see the true uniqueness of the shape.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">''Tertiary structure'': </ins>The second step of protein folding results in the '''tertiary structure''' (or 3° structure). Tertiary structure gives the protein an overall three-dimensional structure. The tertiary structure of a protein is determined by a combination of factors including hydrogen bonds, '''ionic bonds''' (between positively and negatively charged amino acids), '''covalent <ins style="font-weight: bold; text-decoration: none;">bonds</ins>''' '''disulfide bonds''' (between cysteine residues), and '''Van der Waals''' interactions. Tertiary structure can also be affected by repulsive forces between similarly charged amino acids, as well as '''hydrophobic''' and '''hydrophilic''' interactions with a solvent (commonly water). At a distance many proteins form what look to be large globs at this point, and it is only upon more careful and close up inspection that one can see the true uniqueness of the shape.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Intramolecular forces in tertiary structures.png]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Intramolecular forces in tertiary structures.png]]</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figure 3: The various intramolecular interactions that help determine <del style="font-weight: bold; text-decoration: none;">teriary </del>structure</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figure 3: The various intramolecular interactions that help determine <ins style="font-weight: bold; text-decoration: none;">tertiary </ins>structure</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> Proteins may contain only alpha helices, only beta sheets, or a combination of the two. The same holds true for the bonds giving a protein its tertiary structure - all, some or none may be present. These different folding patterns existing in different proteins are what give the proteins their distinctive shapes and sizes. A protein that is 300 amino acids long will be 100 nm as an extended chain. If the protein is an alpha helix, it will be 45 nm long; a beta sheet will be 7 x 7 x 0.8 nm; and a small globular form will form a sphere only 4.5 nm in diameter! </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> Proteins may contain only alpha helices, only beta sheets, or a combination of the two. The same holds true for the bonds giving a protein its tertiary structure - all, some or none may be present. These different folding patterns existing in different proteins are what give the proteins their distinctive shapes and sizes. A protein that is 300 amino acids long will be 100 nm as an extended chain. If the protein is an alpha helix, it will be 45 nm long; a beta sheet will be 7 x 7 x 0.8 nm; and a small globular form will form a sphere only 4.5 nm in diameter! </div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947166&oldid=prevJeremiah C Hagler at 20:01, 15 September 20182018-09-15T20:01:50Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:01, 15 September 2018</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Introduction to Computer-Aided Protein Visualization Lab ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Introduction to Computer-Aided Protein Visualization Lab ==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><StructureSection load='1pgb' size='340' side='right' caption='This simple protein, B1 Immunoglobulin-binding domain of Streptococcal protein G, shows secondary structures nicely. The alpha helix is red, beta sheet in yellow.'<del style="font-weight: bold; text-decoration: none;">> <</del>scene <del style="font-weight: bold; text-decoration: none;">name</del>='79/795987/Pg/1'<del style="font-weight: bold; text-decoration: none;">>Streptococcus protein G</scene</del>></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><StructureSection load='1pgb' size='340' side='right' caption='This simple protein, B1 Immunoglobulin-binding domain of Streptococcal protein G, shows secondary structures nicely. The alpha helix is red, beta sheet in yellow.' scene='79/795987/Pg/1'></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Computer-Aided Protein Visualization Lab ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Computer-Aided Protein Visualization Lab ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Knowing the three-dimensional structure of a protein can be a very powerful tool for biologists. Much can be learned about enzyme function, interaction of molecules in your immune system, the appearance of the surface of viruses, and the interaction of ligands and receptors. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Knowing the three-dimensional structure of a protein can be a very powerful tool for biologists. Much can be learned about enzyme function, interaction of molecules in your immune system, the appearance of the surface of viruses, and the interaction of ligands and receptors. </div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947164&oldid=prevJeremiah C Hagler at 19:55, 15 September 20182018-09-15T19:55:44Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:55, 15 September 2018</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>On the right side of this window you will our first example of a protein represented in three dimensions. This is protein G from the Streptococcal bacterium....a small and very simple polypeptide that binds to antibodies and messes up their organization such that their ability to further activate an immune response is hampered. As you can see in this cartoon representation of protein G, there are two main sub-structures (secondary structure) of this protein. In red is the alpha helix, while a beta sheet is in gold. The regions linking the alpha helix and beta sheets together are called turns or linking regions and are not considered to be discrete secondary structures since they are not tightly structured and tend to be floppy.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>On the right side of this window you will our first example of a protein represented in three dimensions. This is protein G from the Streptococcal bacterium....a small and very simple polypeptide that binds to antibodies and messes up their organization such that their ability to further activate an immune response is hampered. As you can see in this cartoon representation of protein G, there are two main sub-structures (secondary structure) of this protein. In red is the alpha helix, while a beta sheet is in gold. The regions linking the alpha helix and beta sheets together are called turns or linking regions and are not considered to be discrete secondary structures since they are not tightly structured and tend to be floppy.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>1.Alpha helix <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene> Here you can see the alpha helix of protein G in red and in ball and stick representation. The beta sheet is gold, in cartoon representation. Now <del style="font-weight: bold; text-decoration: none;"><scene name='79/795987/Pg/5'></del><scene name='79/795987/Pg/7'>click to view alpha helix in isolation</scene>. Here the alpha helix is completely isolated. The rest of the protein is hidden. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the primary sequence) is shown in red. The '''amino acid side chains''' are shown in tan (each type of amino acid has its own unique side chain, one of 20 different types). If a section of a protein's primary sequence of amino acids forms this coiled structure, it is known as an alpha-helix. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>1.Alpha helix <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene> Here you can see the alpha helix of protein G in red and in ball and stick representation. The beta sheet is gold, in cartoon representation. Now<scene name='79/795987/Pg/7'>click to view alpha helix in isolation</scene>. Here the alpha helix is completely isolated. The rest of the protein is hidden. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the primary sequence) is shown in red. The '''amino acid side chains''' are shown in tan (each type of amino acid has its own unique side chain, one of 20 different types). If a section of a protein's primary sequence of amino acids forms this coiled structure, it is known as an alpha-helix. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>2.Beta sheet <scene name='71/713432/Protein_secondary_structure_bs/2'>Click to see beta sheet</scene><scene name='79/795987/Pg/8'>Click to see beta sheet in isolation</scene></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>2.Beta sheet <scene name='71/713432/Protein_secondary_structure_bs/2'>Click to see beta sheet</scene><scene name='79/795987/Pg/8'>Click to see beta sheet in isolation</scene></div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947163&oldid=prevJeremiah C Hagler at 19:54, 15 September 20182018-09-15T19:54:39Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Introduction to Computer-Aided Protein Visualization Lab ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Introduction to Computer-Aided Protein Visualization Lab ==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><StructureSection load='1pgb' size='340' side='right' caption='This simple protein, B1 Immunoglobulin-binding domain of Streptococcal protein G, shows secondary structures nicely. The alpha helix is red, beta sheet in yellow.<del style="font-weight: bold; text-decoration: none;">' scene='71/713432/Protein_secondary_structure/1</del>'> <scene name='79/795987/Pg/1'>Streptococcus protein G</scene></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><StructureSection load='1pgb' size='340' side='right' caption='This simple protein, B1 Immunoglobulin-binding domain of Streptococcal protein G, shows secondary structures nicely. The alpha helix is red, beta sheet in yellow.'> <scene name='79/795987/Pg/1'>Streptococcus protein G</scene></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Computer-Aided Protein Visualization Lab ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Computer-Aided Protein Visualization Lab ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Knowing the three-dimensional structure of a protein can be a very powerful tool for biologists. Much can be learned about enzyme function, interaction of molecules in your immune system, the appearance of the surface of viruses, and the interaction of ligands and receptors. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Knowing the three-dimensional structure of a protein can be a very powerful tool for biologists. Much can be learned about enzyme function, interaction of molecules in your immune system, the appearance of the surface of viruses, and the interaction of ligands and receptors. </div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947162&oldid=prevJeremiah C Hagler at 19:52, 15 September 20182018-09-15T19:52:05Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:52, 15 September 2018</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Protein folding: </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Protein folding: </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> The most important rule about protein structure is that it is determined by the primary sequence of the protein. Protein folding is a complicated multi-step process. The first step results in the '''secondary structure''' (or <del style="font-weight: bold; text-decoration: none;">2o </del>structure) of the protein. Secondary structures come in two flavors: '''alpha helices''' and '''beta sheets''' (or beta-pleated sheets). Alpha helices are spiral staircase structures (see structure 1 below), and beta-pleated sheets are flat regions where the amino acids run back and forth next to each other in long ribbons (see structure 2 below). These two structures form spontaneously based on the shape/'''hydrophobicity'''/'''charges''' of the amino acids and are held together by '''hydrogen bonds'''. The protein will now look like a string of pearls with twists or zig-zags at intervals along its length.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> The most important rule about protein structure is that it is determined by the primary sequence of the protein. Protein folding is a complicated multi-step process. The first step results in the '''secondary structure''' (or <ins style="font-weight: bold; text-decoration: none;">2° </ins>structure) of the protein. Secondary structures come in two flavors: '''alpha helices''' and '''beta sheets''' (or beta-pleated sheets). Alpha helices are spiral staircase structures (see structure 1 below), and beta-pleated sheets are flat regions where the amino acids run back and forth next to each other in long ribbons (see structure 2 below). These two structures form spontaneously based on the shape/'''hydrophobicity'''/'''charges''' of the amino acids and are held together by '''hydrogen bonds'''. The protein will now look like a string of pearls with twists or zig-zags at intervals along its length.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">1</del>. <del style="font-weight: bold; text-decoration: none;"><scene name='71/713432/Protein_secondary_structure/3'>Click to see alpha helix</scene> <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene><scene name='79/795987/Pg/5'>Click to see alpha helix highlighted</scene></del>In the structure window, click on "Popup" button to open a larger popup window of this structure. You can toggle the spin of the structure on or off by clicking on the "Spin" button. Clicking and holding on the structure in the window will allow you to manipulate the structure, rotating in three-<del style="font-weight: bold; text-decoration: none;">dimensions.</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">For all of the protein structures you will visualize below, once you click on the green link, the structure will appear in the structure window on the right side of the page</ins>. <ins style="font-weight: bold; text-decoration: none;"> </ins>In the structure window, click on "Popup" button to open a larger popup window of this structure. You can toggle the spin of the structure on or off by clicking on the "Spin" button. Clicking and holding on the structure in the window will allow you to manipulate the structure, rotating in three-<ins style="font-weight: bold; text-decoration: none;">dimension</ins>.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> </del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">This is an alpha helix. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the 1o sequence) is shown in pink/red. The '''amino acid side chains''' are shown in yellow (each type of amino acid has its own unique side chain, one of 20 different types). If a section of a protein's primary sequence of amino acids forms this coiled structure, it is known as an alpha-helix</del>. </div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[Put </del>in <del style="font-weight: bold; text-decoration: none;">manipulations </del>of <del style="font-weight: bold; text-decoration: none;">cartoon view </del>to <del style="font-weight: bold; text-decoration: none;">stick, backbone only then backbone with side chains</del>.......<del style="font-weight: bold; text-decoration: none;">adjust color scheme </del>to <del style="font-weight: bold; text-decoration: none;">emphasize secondary structure</del>. <del style="font-weight: bold; text-decoration: none;">Isolate secondary structures if possible</del>, <del style="font-weight: bold; text-decoration: none;">etc]</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">On the right side of this window you will our first example of a protein represented in three dimensions. This is protein G from the Streptococcal bacterium....a small and very simple polypeptide that binds to antibodies and messes up their organization such that their ability to further activate an immune response is hampered. As you can see </ins>in <ins style="font-weight: bold; text-decoration: none;">this cartoon representation </ins>of <ins style="font-weight: bold; text-decoration: none;">protein G, there are two main sub-structures (secondary structure) of this protein. In red is the alpha helix, while a beta sheet is in gold. The regions linking the alpha helix and beta sheets together are called turns or linking regions and are not considered to be discrete secondary structures since they are not tightly structured and tend </ins>to <ins style="font-weight: bold; text-decoration: none;">be floppy</ins>.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2. <scene name='71/713432/Protein_secondary_structure_bs/2'>Click to see beta sheet</scene><scene name='79/795987/Pg/8'>Click to see beta sheet in isolation</scene></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">1</ins>.<ins style="font-weight: bold; text-decoration: none;">Alpha helix <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene> Here you can see the alpha helix of protein G in red and in ball and stick representation</ins>. <ins style="font-weight: bold; text-decoration: none;"> The beta sheet is gold, in cartoon representation</ins>. <ins style="font-weight: bold; text-decoration: none;"> Now <scene name='79/795987/Pg/5'><scene name='79/795987/Pg/7'>click to view alpha helix in isolation</scene></ins>. <ins style="font-weight: bold; text-decoration: none;"> Here the alpha helix is completely isolated</ins>. <ins style="font-weight: bold; text-decoration: none;"> The rest of the protein is hidden</ins>. <ins style="font-weight: bold; text-decoration: none;">The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' </ins>to <ins style="font-weight: bold; text-decoration: none;">form the primary sequence) is shown in red. The '''amino acid side chains''' are shown in tan (each type of amino acid has its own unique side chain, one of 20 different types)</ins>. <ins style="font-weight: bold; text-decoration: none;">If a section of a protein's primary sequence of amino acids forms this coiled structure</ins>, <ins style="font-weight: bold; text-decoration: none;">it is known as an alpha-helix. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2.<ins style="font-weight: bold; text-decoration: none;">Beta sheet </ins><scene name='71/713432/Protein_secondary_structure_bs/2'>Click to see beta sheet</scene><scene name='79/795987/Pg/8'>Click to see beta sheet in isolation</scene></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> The second step of protein folding results in the '''tertiary structure''' (or 3° structure). Tertiary structure gives the protein an overall three-dimensional structure. The tertiary structure of a protein is determined by a combination of factors including hydrogen bonds, '''ionic bonds''' (between positively and negatively charged amino acids), '''covalent''' '''disulfide bonds''' (between cysteine residues), and '''Van der Waals''' interactions. Tertiary structure can also be affected by repulsive forces between similarly charged amino acids, as well as '''hydrophobic''' and '''hydrophilic''' interactions with a solvent (commonly water). At a distance many proteins form what look to be large globs at this point, and it is only upon more careful and close up inspection that one can see the true uniqueness of the shape.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> The second step of protein folding results in the '''tertiary structure''' (or 3° structure). Tertiary structure gives the protein an overall three-dimensional structure. The tertiary structure of a protein is determined by a combination of factors including hydrogen bonds, '''ionic bonds''' (between positively and negatively charged amino acids), '''covalent''' '''disulfide bonds''' (between cysteine residues), and '''Van der Waals''' interactions. Tertiary structure can also be affected by repulsive forces between similarly charged amino acids, as well as '''hydrophobic''' and '''hydrophilic''' interactions with a solvent (commonly water). At a distance many proteins form what look to be large globs at this point, and it is only upon more careful and close up inspection that one can see the true uniqueness of the shape.</div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947156&oldid=prevJeremiah C Hagler at 18:56, 15 September 20182018-09-15T18:56:50Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> The most important rule about protein structure is that it is determined by the primary sequence of the protein. Protein folding is a complicated multi-step process. The first step results in the '''secondary structure''' (or 2o structure) of the protein. Secondary structures come in two flavors: '''alpha helices''' and '''beta sheets''' (or beta-pleated sheets). Alpha helices are spiral staircase structures (see structure 1 below), and beta-pleated sheets are flat regions where the amino acids run back and forth next to each other in long ribbons (see structure 2 below). These two structures form spontaneously based on the shape/'''hydrophobicity'''/'''charges''' of the amino acids and are held together by '''hydrogen bonds'''. The protein will now look like a string of pearls with twists or zig-zags at intervals along its length.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> The most important rule about protein structure is that it is determined by the primary sequence of the protein. Protein folding is a complicated multi-step process. The first step results in the '''secondary structure''' (or 2o structure) of the protein. Secondary structures come in two flavors: '''alpha helices''' and '''beta sheets''' (or beta-pleated sheets). Alpha helices are spiral staircase structures (see structure 1 below), and beta-pleated sheets are flat regions where the amino acids run back and forth next to each other in long ribbons (see structure 2 below). These two structures form spontaneously based on the shape/'''hydrophobicity'''/'''charges''' of the amino acids and are held together by '''hydrogen bonds'''. The protein will now look like a string of pearls with twists or zig-zags at intervals along its length.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>1. <scene name='71/713432/Protein_secondary_structure/3'>Click to see alpha helix</scene> In the structure window, click on "Popup" button to open a larger popup window of this structure. You can toggle the spin of the structure on or off by clicking on the "Spin" button. Clicking and holding on the structure in the window will allow you to manipulate the structure, rotating in three-dimensions.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>1. <scene name='71/713432/Protein_secondary_structure/3'>Click to see alpha helix<ins style="font-weight: bold; text-decoration: none;"></scene> <scene name='79/795987/Pg/9'>Click to see alpha helix in relation to beta sheet</scene><scene name='79/795987/Pg/5'>Click to see alpha helix highlighted</ins></scene>In the structure window, click on "Popup" button to open a larger popup window of this structure. You can toggle the spin of the structure on or off by clicking on the "Spin" button. Clicking and holding on the structure in the window will allow you to manipulate the structure, rotating in three-dimensions.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This is an alpha helix. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the 1o sequence) is shown in pink/red. The '''amino acid side chains''' are shown in yellow (each type of amino acid has its own unique side chain, one of 20 different types). If a section of a protein's primary sequence of amino acids forms this coiled structure, it is known as an alpha-helix. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This is an alpha helix. The '''amino acid backbone''' (the parts of the amino acids that are linked together by a '''peptide bond''' to form the 1o sequence) is shown in pink/red. The '''amino acid side chains''' are shown in yellow (each type of amino acid has its own unique side chain, one of 20 different types). If a section of a protein's primary sequence of amino acids forms this coiled structure, it is known as an alpha-helix. </div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947153&oldid=prevJeremiah C Hagler at 18:46, 15 September 20182018-09-15T18:46:57Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2. <scene name='71/713432/Protein_secondary_structure_bs/2'>Click to see beta sheet</scene></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2. <scene name='71/713432/Protein_secondary_structure_bs/2'>Click to see beta sheet<ins style="font-weight: bold; text-decoration: none;"></scene><scene name='79/795987/Pg/8'>Click to see beta sheet in isolation</ins></scene></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> The second step of protein folding results in the '''tertiary structure''' (or 3° structure). Tertiary structure gives the protein an overall three-dimensional structure. The tertiary structure of a protein is determined by a combination of factors including hydrogen bonds, '''ionic bonds''' (between positively and negatively charged amino acids), '''covalent''' '''disulfide bonds''' (between cysteine residues), and '''Van der Waals''' interactions. Tertiary structure can also be affected by repulsive forces between similarly charged amino acids, as well as '''hydrophobic''' and '''hydrophilic''' interactions with a solvent (commonly water). At a distance many proteins form what look to be large globs at this point, and it is only upon more careful and close up inspection that one can see the true uniqueness of the shape.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> The second step of protein folding results in the '''tertiary structure''' (or 3° structure). Tertiary structure gives the protein an overall three-dimensional structure. The tertiary structure of a protein is determined by a combination of factors including hydrogen bonds, '''ionic bonds''' (between positively and negatively charged amino acids), '''covalent''' '''disulfide bonds''' (between cysteine residues), and '''Van der Waals''' interactions. Tertiary structure can also be affected by repulsive forces between similarly charged amino acids, as well as '''hydrophobic''' and '''hydrophilic''' interactions with a solvent (commonly water). At a distance many proteins form what look to be large globs at this point, and it is only upon more careful and close up inspection that one can see the true uniqueness of the shape.</div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947152&oldid=prevJeremiah C Hagler at 18:01, 15 September 20182018-09-15T18:01:44Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Introduction to Computer-Aided Protein Visualization Lab ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Introduction to Computer-Aided Protein Visualization Lab ==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><StructureSection load='1pgb' size='340' side='right' caption='This simple protein, B1 Immunoglobulin-binding domain of Streptococcal protein G, shows secondary structures nicely. The alpha helix is red, beta sheet in yellow.' scene='71/713432/Protein_secondary_structure/1'></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><StructureSection load='1pgb' size='340' side='right' caption='This simple protein, B1 Immunoglobulin-binding domain of Streptococcal protein G, shows secondary structures nicely. The alpha helix is red, beta sheet in yellow.' scene='71/713432/Protein_secondary_structure/1'<ins style="font-weight: bold; text-decoration: none;">> <scene name='79/795987/Pg/1'>Streptococcus protein G</scene</ins>></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Computer-Aided Protein Visualization Lab ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Computer-Aided Protein Visualization Lab ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Knowing the three-dimensional structure of a protein can be a very powerful tool for biologists. Much can be learned about enzyme function, interaction of molecules in your immune system, the appearance of the surface of viruses, and the interaction of ligands and receptors. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Knowing the three-dimensional structure of a protein can be a very powerful tool for biologists. Much can be learned about enzyme function, interaction of molecules in your immune system, the appearance of the surface of viruses, and the interaction of ligands and receptors. </div></td></tr>
</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947151&oldid=prevJeremiah C Hagler at 17:51, 15 September 20182018-09-15T17:51:54Z<p></p>
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</table>Jeremiah C Haglerhttps://proteopedia.org/index.php?title=Phillips_Academy_Computer-Aided_Protein_Visualization_Lab&diff=2947149&oldid=prevJeremiah C Hagler: User:Jeremiah C Hagler/Protein 1 Modified moved to Phillips Academy Computer-Aided Protein Visualization Lab2018-09-15T17:45:07Z<p><a href="/User:Jeremiah_C_Hagler/Protein_1_Modified" class="mw-redirect" title="User:Jeremiah C Hagler/Protein 1 Modified">User:Jeremiah C Hagler/Protein 1 Modified</a> moved to <a href="/Phillips_Academy_Computer-Aided_Protein_Visualization_Lab" title="Phillips Academy Computer-Aided Protein Visualization Lab">Phillips Academy Computer-Aided Protein Visualization Lab</a></p>
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</td></tr></table>Jeremiah C Hagler