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I326T - Revision history
2024-03-28T11:56:35Z
Revision history for this page on the wiki
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Demel: /* Conclusion */
2011-08-11T19:55:38Z
<p><span dir="auto"><span class="autocomment">Conclusion</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:55, 11 August 2011</td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Conclusion ===</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Conclusion ===</div></td>
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<td style="color: #222; 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;"></td>
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<td style="color: #222; 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 overall trend of the calculated energies stays the same. FoldX calculated an energy difference of 7% between the wildtype and the mutated protein structure and both the minimise and the Gromacs energies are a lot lower for the mutated protein structures than for the wildtype structures. Looking at the structure and the biophysical properties of the mutating residues, which lead to the formation of hydrogen bonds, we can see that isoleucine and threonine are quite similar concerning these aspects. The same structure and the hydrogen bond network that didn't change could be an explanation for repeating expected energy values.</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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<td style="background-color: #f8f9fa; color: #222; 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>return to [[Structure-based_mutation_analysis_BCKDHA| Structure-based mutation analysis]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>return to [[Structure-based_mutation_analysis_BCKDHA| Structure-based mutation analysis]]</div></td>
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Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=I326T&diff=10779&oldid=prev
Demel: /* Side chain properties */
2011-08-11T18:15:15Z
<p><span dir="auto"><span class="autocomment">Side chain properties</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:15, 11 August 2011</td>
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<td style="background-color: #f8f9fa; color: #222; 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>|[[File:Mutation7_BCKDHAMinimise.png|thumb|Figure 3: Structure of threonine on position 326 in the mutated protein]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>|[[File:Mutation7_BCKDHAMinimise.png|thumb|Figure 3: Structure of threonine on position 326 in the mutated protein]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>
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<td style="color: #222; 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;"></td>
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<td style="color: #222; 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>This substitution does not change very much in the amino acid structure but in the biochemical properties of the amino acids. Isoleucine is aliphatic and hydrophobic and therefore well suited for being in the inside of the protein. The mutation to Threonine introduces a hydroxylic, polar amino acids, which might cause instability of the protein.</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Hydrogen Bonding network ===</div></td>
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Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=I326T&diff=10778&oldid=prev
Demel: /* Mapping onto crystal structure */
2011-08-11T18:12:33Z
<p><span dir="auto"><span class="autocomment">Mapping onto crystal structure</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:12, 11 August 2011</td>
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<td style="background-color: #f8f9fa; color: #222; 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>Figure 1 shows the protein structure with highlighted amino acids. The mutation position is colored violet, the thiamine pyrophosphate binding sites are orange, and metal binding sites are yellow.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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>Figure 1 shows the protein structure with highlighted amino acids. The mutation position is colored violet, the thiamine pyrophosphate binding sites are orange, and metal binding sites are yellow.</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>[[File:BCKDHA_mut7.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]]</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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>[[File:BCKDHA_mut7.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]]</div></td>
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<td class="diff-marker">+</td>
<td style="color: #222; 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>Looking at figure 1 it is not obvious why this mutation should be damaging, as it is not nearby the active center. The mutation does also not take place on the surface of the protein. So we have to take a look at the side chain properties to understand the damaging effect of this mutation.</div></td>
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<td style="color: #222; 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;"></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Side chain properties ===</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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>=== Side chain properties ===</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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>Figures 2 and 3 show the superposition of the mutated amino acid with the wildtype. The pictures showing the wildtype structure display the unmutated residue in bold and vice versa.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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>Figures 2 and 3 show the superposition of the mutated amino acid with the wildtype. The pictures showing the wildtype structure display the unmutated residue in bold and vice versa.</div></td>
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Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=I326T&diff=10627&oldid=prev
Demel: /* Structure-based Mutation Analysis */
2011-08-11T11:34:10Z
<p><span dir="auto"><span class="autocomment">Structure-based Mutation Analysis</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:34, 11 August 2011</td>
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<td style="background-color: #f8f9fa; color: #222; 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>== Structure-based Mutation Analysis ==</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>== Structure-based Mutation Analysis ==</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Mapping onto crystal structure ===</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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>=== Mapping onto crystal structure ===</div></td>
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<td style="color: #222; 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 1 shows the protein structure with highlighted amino acids. The mutation position is colored violet, the thiamine pyrophosphate binding sites are orange, and metal binding sites are yellow.</div></td>
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<td style="color: #222; 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;"></td>
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<td style="color: #222; 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>[[File:BCKDHA_mut7.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Side chain properties ===</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Side chain properties ===</div></td>
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<td class="diff-marker">+</td>
<td style="color: #222; 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>Figures 2 and 3 show the superposition of the mutated amino acid with the wildtype. The pictures showing the wildtype structure display the unmutated residue in bold and vice versa.</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=I326T&diff=10600&oldid=prev
Demel: /* Hydrogen Bonding network */
2011-08-11T11:22:10Z
<p><span dir="auto"><span class="autocomment">Hydrogen Bonding network</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:22, 11 August 2011</td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Hydrogen Bonding network ===</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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>=== Hydrogen Bonding network ===</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; 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 following figures show the hydrogen bonds between the wildtype residue and its environment compared to the formation of hydrogen bonds when the corresponding residue is mutated.</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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<td style="color: #222; 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>Hydrogen bonds are interactions between an hydrogen atom and an electronegative atom. Electronegative atoms which often take part in hydrogen bonds are oxygen, nitrogen and fluorine (not present in amino acid side chains). They serve as a hydrogen bond acceptor, whereas a hydrogen bond donor is a electronegative atom bonded to a hydrogen atom.</div></td>
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<td style="color: #222; 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>Hydrogen bonds are essential for the three-dimensional structures of proteins. They play a important role in the formation of helices and beta-sheets and cause proteins to fold into a specific structure.</div></td>
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<td style="background-color: #f8f9fa; color: #222; 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;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; 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;"></td>
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<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; 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>Showing hydrogen bonds with Pymol: A -> find -> polar contacts -> within selection</div></td>
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<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; 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 respective amino acids were colored by element, s.t. oxygen is red, nitrogen is blue, hydrogen is white and sulfur is yellow.</div></td>
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<td class="diff-marker">+</td>
<td style="color: #222; 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;"></td>
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<td style="color: #222; 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 following figures show the hydrogen bonds between the wildtype residue and its environment compared to the formation of hydrogen bonds when the corresponding residue is mutated.</div></td>
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Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=I326T&diff=10543&oldid=prev
Demel: Created page with "== Structure-based Mutation Analysis == === Mapping onto crystal structure === === Side chain properties === {|class="centered" |[[File:Wildtype7_BCKDHAMinimise.png|thumb|Figu…"
2011-08-11T09:41:55Z
<p>Created page with "== Structure-based Mutation Analysis == === Mapping onto crystal structure === === Side chain properties === {|class="centered" |[[File:Wildtype7_BCKDHAMinimise.png|thumb|Figu…"</p>
<p><b>New page</b></p><div>== Structure-based Mutation Analysis ==<br />
=== Mapping onto crystal structure ===<br />
<br />
=== Side chain properties ===<br />
<br />
<br />
{|class="centered"<br />
|[[File:Wildtype7_BCKDHAMinimise.png|thumb|Figure 2: Structure of isoleucine on position 326 in the wildtype protein]]<br />
|[[File:Mutation7_BCKDHAMinimise.png|thumb|Figure 3: Structure of threonine on position 326 in the mutated protein]]<br />
|}<br />
<br />
=== Hydrogen Bonding network ===<br />
The following figures show the hydrogen bonds between the wildtype residue and its environment compared to the formation of hydrogen bonds when the corresponding residue is mutated.<br />
<br />
<br />
<br />
{|class="centered"<br />
|[[File:BCKDHA_Wt281.png|thumb|150px|Figure 4: Hydrogen Bonds for isoleucine on pos 326 in the wild type structure]]<br />
|[[File:BCKDHA_Mut281.png|thumb|150px|Figure 5: Hydrogen Bonds for threonine on pos 326 in the mutated type structure]]<br />
|}<br />
The mutation from isoleucine to threonine doesn't have an influence on the hydrogen bonding network, although the oxygen atom of threonine could serve as an additional hydrogen bond donor (compare Figure 4 and 5).<br />
<br />
===foldX Energy Comparison===<br />
We used the foldX tool to compare the energy of the wildtype protein and the mutated structure. The following table shows the calculated energy values as well as the percentage of difference, to compare the energy calculations with other tools:<br />
<br />
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"<br />
!Energy<br />
!wildtype energy<br />
!total energy of mutated protein<br />
!difference<br />
|-<br />
|absolute||401.00||432.94||31.94<br />
|-<br />
|relative||100%||107%||7%<br />
|}<br />
<br />
The total energy of the mutated structure is a little bit higher than the energy of the wildtype protein structure. As protein energies should be low for a stable protein, the increasing energy leads to the assumption that this mutation might be damaging for the protein structure.<br />
<br />
===minimise Energy Comparison===<br />
<br />
Next we used the minimise tool to compare the energy of the wildtype protein and the mutated structure. The following table shows the calculated energy values as well as the percentage of difference, to compare the energy calculations with other tools:<br />
<br />
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"<br />
!Energy<br />
!wildtype energy<br />
!total energy of mutated protein<br />
!difference<br />
|-<br />
|absolute|| -2485.452755||-4317.105618||-1831.652863<br />
|-<br />
|relative|| 100%||57%||43%<br />
|}<br />
<br />
The mutated structure has an energy that is much smaller than the wildtype<br />
<br />
===gromacs Energy comparison===<br />
<br />
The Gromacs energy comparison was conducted using the AMBER03 force field. The following table shows the calculated energies for the wildtype protein structure.<br />
<br />
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"<br />
!Energy<br />
!Average<br />
!Err.Est<br />
!RMSD<br />
!Tot-Drift (kJ/mol)<br />
|-<br />
|Bond || 3072.83 || 2200||-nan||-13100.2<br />
|-<br />
|Angle || 3616.97||230|| -nan||-1295.57<br />
|-<br />
|Potential || 2.67001e+07 ||2.6e+07||-nan||-1.60382e+08<br />
|}<br />
<br />
Here are the results for the mutated protein structure.<br />
<br />
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"<br />
!Energy<br />
!Average<br />
!Err.Est<br />
!RMSD<br />
!Tot-Drift (kJ/mol)<br />
|-<br />
|Bond || 3214.03||2300||7364.47||-13490.1<br />
|-<br />
|Angle || 3738.44||310||698.943||-1792.01<br />
|-<br />
|Potential || 7.29e+06||6.9e+06||8.86e+07||-4.38e+07<br />
|}<br />
<br />
<br />
As we want to compare the Gromacs energies with the other tools, we calculate the ratio of difference considering the potential energy:<br />
<br />
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"<br />
!Energy<br />
!wildtype energy<br />
!total energy of mutated protein<br />
!difference<br />
|-<br />
|absolute|| 2.67001e+07||7.29e+06||-19410100<br />
|-<br />
|relative|| 100%||27%||73%<br />
|}<br />
<br />
The calculated energy for the mutated structure is much smaller than for the wildtype structure.<br />
<br />
=== Conclusion ===<br />
<br />
return to [[Structure-based_mutation_analysis_BCKDHA| Structure-based mutation analysis]]</div>
Demel