https://proteopedia.org/index.php?action=history&feed=atom&title=Michael_Pikaart%2FBiochem_StructureIntro
Michael Pikaart/Biochem StructureIntro - Revision history
2026-10-10T23:53:25Z
Revision history for this page on the wiki
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https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1119168&oldid=prev
Michael Pikaart at 00:05, 12 September 2010
2010-09-12T00:05:07Z
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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;"><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>Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4<del style="font-weight: bold; text-decoration: none;">|SGD</del>]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.</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>Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.</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>Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.</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>Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.</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>Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /></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>Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /></div></td></tr>
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Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116386&oldid=prev
Michael Pikaart at 13:10, 30 August 2010
2010-08-30T13:10:56Z
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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;"><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><scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>A <del style="font-weight: bold; text-decoration: none;">Beta </del>turn linking two anti-parallel beta strands</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</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><scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>A <ins style="font-weight: bold; text-decoration: none;">beta </ins>turn linking two anti-parallel beta strands</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</div></td></tr>
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Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116385&oldid=prev
Michael Pikaart at 13:05, 30 August 2010
2010-08-30T13:05:23Z
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<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><scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'><del style="font-weight: bold; text-decoration: none;">TextToBeDisplayed</del></scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</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><scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'><ins style="font-weight: bold; text-decoration: none;">A Beta turn linking two anti-parallel beta strands</ins></scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</div></td></tr>
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Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116384&oldid=prev
Michael Pikaart at 13:03, 30 August 2010
2010-08-30T13:03:06Z
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<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><scene name='<del style="font-weight: bold; text-decoration: none;">Pikaart_Sandbox_1</del>/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</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><scene name='<ins style="font-weight: bold; text-decoration: none;">Michael_Pikaart/Biochem_StructureIntro</ins>/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</scene><ins style="font-weight: bold; text-decoration: none;">: Here the beta sheet strands of elastase are highlighted. You can see the emergence of the higher-order domains formed within the protein's structure.</ins></div></td></tr>
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<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;"><scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>TextToBeDisplayed</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</ins></div></td></tr>
</table>
Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116383&oldid=prev
Michael Pikaart at 12:27, 30 August 2010
2010-08-30T12:27:23Z
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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;"><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><scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/<del style="font-weight: bold; text-decoration: none;">1</del>'>Beta sheet sections from elastase</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><scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/<ins style="font-weight: bold; text-decoration: none;">2</ins>'>Beta sheet sections from elastase</scene></div></td></tr>
</table>
Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114435&oldid=prev
Michael Pikaart: Pikaart Sandbox 1 moved to Michael Pikaart/Biochem StructureIntro
2010-08-23T17:41:20Z
<p><a href="/index.php?title=Pikaart_Sandbox_1&action=edit&redlink=1" class="new" title="Pikaart Sandbox 1 (page does not exist)">Pikaart Sandbox 1</a> moved to <a href="/Michael_Pikaart/Biochem_StructureIntro" title="Michael Pikaart/Biochem StructureIntro">Michael Pikaart/Biochem StructureIntro</a></p>
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<td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:41, 23 August 2010</td>
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Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114434&oldid=prev
Michael Pikaart at 17:38, 23 August 2010
2010-08-23T17:38:40Z
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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>Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</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>Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</div></td></tr>
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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;"><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;"><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>
</table>
Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114433&oldid=prev
Michael Pikaart at 17:31, 23 August 2010
2010-08-23T17:31:30Z
<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 17:31, 23 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</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> </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>Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</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>Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</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>
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<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><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><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><ins style="font-weight: bold; text-decoration: none;"></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;"><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;"><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>== Beta sheet ==</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>== Beta sheet ==</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>A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='<del style="font-weight: bold; text-decoration: none;">est1</del>' size='400' frame='true' align='right' caption='Insert caption here' /></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>A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='<ins style="font-weight: bold; text-decoration: none;">1est</ins>' size='400' frame='true' align='right' caption='Insert caption here' /<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> </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><ins style="font-weight: bold; text-decoration: none;"><scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/1'>Beta sheet sections from elastase</scene</ins>></div></td></tr>
</table>
Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114432&oldid=prev
Michael Pikaart at 17:25, 23 August 2010
2010-08-23T17:25:29Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<col class="diff-marker" />
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:25, 23 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l31">Line 31:</td>
<td colspan="2" class="diff-lineno">Line 31:</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>== Beta sheet ==</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>== Beta sheet ==</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><ins style="font-weight: bold; text-decoration: none;">A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='est1' size='400' frame='true' align='right' caption='Insert caption here' /></ins></div></td></tr>
</table>
Michael Pikaart
https://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114431&oldid=prev
Michael Pikaart at 17:17, 23 August 2010
2010-08-23T17:17:10Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:17, 23 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l17">Line 17:</td>
<td colspan="2" class="diff-lineno">Line 17:</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>Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /></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>Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /></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><scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene> <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><scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene></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 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>Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."</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>Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."</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><scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene> <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><scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene></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 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 scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?</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 scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?</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><scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene> <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><scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene></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 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>Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</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>Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</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><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><ins style="font-weight: bold; text-decoration: none;">== Beta sheet ==</ins></div></td></tr>
</table>
Michael Pikaart