https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&feed=atom&action=history
C264W - Revision history
2024-03-29T09:00:29Z
Revision history for this page on the wiki
MediaWiki 1.31.16
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10811&oldid=prev
Demel: /* foldX Energy Comparison */
2011-08-11T19:47:01Z
<p><span dir="auto"><span class="autocomment">foldX Energy Comparison</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:47, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 46:</td>
<td colspan="2" class="diff-lineno">Line 46:</td>
</tr>
<tr>
<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>|}</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>|}</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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 total energy of the mutated structure is a <del class="diffchange diffchange-inline">little bit</del> higher than the energy of the wildtype protein structure. <del class="diffchange diffchange-inline">As</del> <del class="diffchange diffchange-inline">protein</del> <del class="diffchange diffchange-inline">energies</del> <del class="diffchange diffchange-inline">should</del> <del class="diffchange diffchange-inline">be</del> <del class="diffchange diffchange-inline">low</del> <del class="diffchange diffchange-inline">for</del> <del class="diffchange diffchange-inline">a</del> <del class="diffchange diffchange-inline">stable</del> protein<del class="diffchange diffchange-inline">,</del> the <del class="diffchange diffchange-inline">increasing</del> <del class="diffchange diffchange-inline">energy</del> <del class="diffchange diffchange-inline">leads</del> <del class="diffchange diffchange-inline">to</del> the <del class="diffchange diffchange-inline">assumption</del> <del class="diffchange diffchange-inline">that</del> this mutation might <del class="diffchange diffchange-inline">be</del> <del class="diffchange diffchange-inline">damaging</del> <del class="diffchange diffchange-inline">for</del> the protein <del class="diffchange diffchange-inline">structure</del>.</div></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 total energy of the mutated structure is a <ins class="diffchange diffchange-inline">lot</ins> higher than the energy of the wildtype protein structure. <ins class="diffchange diffchange-inline">This</ins> <ins class="diffchange diffchange-inline">indicates</ins> <ins class="diffchange diffchange-inline">that</ins> <ins class="diffchange diffchange-inline">this</ins> <ins class="diffchange diffchange-inline">mutation</ins> <ins class="diffchange diffchange-inline">has</ins> <ins class="diffchange diffchange-inline">an</ins> <ins class="diffchange diffchange-inline">enormous</ins> <ins class="diffchange diffchange-inline">effect on the stability of the</ins> protein<ins class="diffchange diffchange-inline">. As changing</ins> the <ins class="diffchange diffchange-inline">stability</ins> <ins class="diffchange diffchange-inline">of</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">protein goes along with</ins> the <ins class="diffchange diffchange-inline">function</ins> <ins class="diffchange diffchange-inline">of the protein,</ins> this mutation might <ins class="diffchange diffchange-inline">very</ins> <ins class="diffchange diffchange-inline">likely</ins> <ins class="diffchange diffchange-inline">affect</ins> the protein<ins class="diffchange diffchange-inline">'s</ins> <ins class="diffchange diffchange-inline">function</ins>.</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>===minimise Energy Comparison===</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>===minimise Energy Comparison===</div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-10809:rev-10811:1.7.3:0 -->
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10809&oldid=prev
Demel: /* Conclusion */
2011-08-11T19:37:45Z
<p><span dir="auto"><span class="autocomment">Conclusion</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:37, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 117:</td>
<td colspan="2" class="diff-lineno">Line 117:</td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>=== Conclusion ===</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>=== Conclusion ===</div></td>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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>This time the calculations of the different tools disagree completely. While foldX again predicted a higher energy (as for all the other mutations under consideration) and the minimise energy is still lower than for the wildtype structure, Gromacs now calculated a very high energy for the mutated structure compared to the wildtype structure. As a higher energy usually indicates a protein that is more instabile that a protein with lower energy, one could easily argue that this mutation is delerious. This statement does not agree with the calculations from foldX and minimise. The structural differences of the amino acids however are a strong indication for the deleterious effect of this mutation, that leads to instability of the protein structure and therefore affects the protein's function.</div></td>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>return to [[Structure-based_mutation_analysis_BCKDHA| Structure-based mutation analysis]]</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>return to [[Structure-based_mutation_analysis_BCKDHA| Structure-based mutation analysis]]</div></td>
</tr>
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10808&oldid=prev
Demel: /* gromacs Energy comparison */
2011-08-11T19:33:41Z
<p><span dir="auto"><span class="autocomment">gromacs Energy comparison</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:33, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 114:</td>
<td colspan="2" class="diff-lineno">Line 114:</td>
</tr>
<tr>
<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>|}</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>|}</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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><del class="diffchange diffchange-inline">The</del> calculated energy for the mutated structure is higher than for the wildtype structure.</div></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><ins class="diffchange diffchange-inline">Interestingly, the</ins> calculated energy for the mutated structure is higher than for<ins class="diffchange diffchange-inline"> the wildtype structure, leading to the assumption that the mutated structure is more instabile than</ins> the wildtype structure.</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>=== Conclusion ===</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>=== Conclusion ===</div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-10807:rev-10808:1.7.3:0 -->
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10807&oldid=prev
Demel: /* minimise Energy Comparison */
2011-08-11T19:31:22Z
<p><span dir="auto"><span class="autocomment">minimise Energy Comparison</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:31, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 63:</td>
<td colspan="2" class="diff-lineno">Line 63:</td>
</tr>
<tr>
<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>|}</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>|}</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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><del class="diffchange diffchange-inline">The</del> <del class="diffchange diffchange-inline">mutated</del> <del class="diffchange diffchange-inline">structure has</del> an energy <del class="diffchange diffchange-inline">that</del> <del class="diffchange diffchange-inline">is</del> <del class="diffchange diffchange-inline">much</del> <del class="diffchange diffchange-inline">smaller</del> than the wildtype</div></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><ins class="diffchange diffchange-inline">Minimise</ins> <ins class="diffchange diffchange-inline">calculated</ins> <ins class="diffchange diffchange-inline">again</ins> an<ins class="diffchange diffchange-inline"> much lower</ins> energy <ins class="diffchange diffchange-inline">for</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">mutated</ins> <ins class="diffchange diffchange-inline">structure</ins> than<ins class="diffchange diffchange-inline"> for</ins> the wildtype<ins class="diffchange diffchange-inline"> structure.</ins></div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>===gromacs Energy comparison===</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>===gromacs Energy comparison===</div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-10775:rev-10807:1.7.3:0 -->
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10775&oldid=prev
Demel: /* Side chain properties */
2011-08-11T18:05:51Z
<p><span dir="auto"><span class="autocomment">Side chain properties</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:05, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 14:</td>
<td colspan="2" class="diff-lineno">Line 14:</td>
</tr>
<tr>
<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:Mutation5_BCKDHAMinimise.png|thumb|Figure 3: Structure of tryptophan on position 264 in the mutated protein]]</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:Mutation5_BCKDHAMinimise.png|thumb|Figure 3: Structure of tryptophan on position 264 in the mutated protein]]</div></td>
</tr>
<tr>
<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>|}</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>|}</div></td>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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>Looking at figures 2 and 3 it is obvious that this substitution is harmful to the protein's function. This mutation has a huge impact on the structure and physiochemical properties of the amino acid at this position. A small, sulphur-containing amino acid is replaced by an aromatic amino acid, which occupies a lot more space. The hydrophobicity and polarity remain the same, nevertheless are the amino acids very different and this mutation will destroy the protein's function.</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>=== Hydrogen Bonding network ===</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>=== Hydrogen Bonding network ===</div></td>
</tr>
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10774&oldid=prev
Demel: /* Mapping onto crystal structure */
2011-08-11T18:04:37Z
<p><span dir="auto"><span class="autocomment">Mapping onto crystal structure</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:04, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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_mut5.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_mut5.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]]</div></td>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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 position of this mutation is relatively close by the active sites in the protein. With the knowledge that the compact amino acid cysteine is replaced by a very bulky tryptophan the fact, that this mutation could disturb the binding of ligands should not be excluded.</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>
<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>
</tr>
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10628&oldid=prev
Demel: /* Mapping onto crystal structure */
2011-08-11T11:34:19Z
<p><span dir="auto"><span class="autocomment">Mapping onto crystal structure</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:34, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>[[File:BCKDHA_mut5.png|thumb|center| Figure 1: Structure of <del class="diffchange diffchange-inline">tyrosine on position 82</del> <del class="diffchange diffchange-inline">in</del> <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">wildtype</del> <del class="diffchange diffchange-inline">protein</del>]]</div></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>[[File:BCKDHA_mut5.png|thumb|center| Figure 1:<ins class="diffchange diffchange-inline"> </ins> Structure of <ins class="diffchange diffchange-inline">BCKDHA</ins> <ins class="diffchange diffchange-inline">with</ins> <ins class="diffchange diffchange-inline">highlighted</ins> <ins class="diffchange diffchange-inline">amino</ins> <ins class="diffchange diffchange-inline">acids</ins>]]</div></td>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>
</tr>
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10619&oldid=prev
Demel: /* Structure-based Mutation Analysis */
2011-08-11T11:32:41Z
<p><span dir="auto"><span class="autocomment">Structure-based Mutation Analysis</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:32, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td>
</tr>
<tr>
<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>== Structure-based Mutation Analysis ==</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>== Structure-based Mutation Analysis ==</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>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>
</tr>
<tr>
<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;"></td>
<td colspan="2" class="diff-empty"> </td>
</tr>
<tr>
<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>[[File:BCKDHA_mut5.png|thumb|center| Figure 1: Structure of tyrosine on position 82 in the wildtype protein]]</div></td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>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>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>
<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>
</tr>
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10598&oldid=prev
Demel: /* Hydrogen Bonding network */
2011-08-11T11:21:57Z
<p><span dir="auto"><span class="autocomment">Hydrogen Bonding network</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:21, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 11:</td>
<td colspan="2" class="diff-lineno">Line 11:</td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>=== Hydrogen Bonding network ===</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>=== Hydrogen Bonding network ===</div></td>
</tr>
<tr>
<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>
<td colspan="2" class="diff-empty"> </td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>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>
</tr>
<tr>
<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>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>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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>
</tr>
<tr>
<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>
</tr>
<tr>
<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;"></td>
</tr>
<tr>
<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 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>
</tr>
<tr>
<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>{|class="centered"</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>{|class="centered"</div></td>
</tr>
<tr>
<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_Wt219.png|thumb|150px|Figure 4: Hydrogen Bonds for cysteine on pos 264 in the wild type 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>|[[File:BCKDHA_Wt219.png|thumb|150px|Figure 4: Hydrogen Bonds for cysteine on pos 264 in the wild type structure]]</div></td>
</tr>
</table>
Demel
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=C264W&diff=10538&oldid=prev
Demel: Created page with "== Structure-based Mutation Analysis == === Mapping onto crystal structure === === Side chain properties === {|class="centered" |[[File:Wildtype5_BCKDHAMinimise.png|thumb|Figu…"
2011-08-11T09:37:09Z
<p>Created page with "== Structure-based Mutation Analysis == === Mapping onto crystal structure === === Side chain properties === {|class="centered" |[[File:Wildtype5_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:Wildtype5_BCKDHAMinimise.png|thumb|Figure 2: Structure of cysteine on position 264 in the wildtype protein]]<br />
|[[File:Mutation5_BCKDHAMinimise.png|thumb|Figure 3: Structure of tryptophan on position 264 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 />
{|class="centered"<br />
|[[File:BCKDHA_Wt219.png|thumb|150px|Figure 4: Hydrogen Bonds for cysteine on pos 264 in the wild type structure]]<br />
|[[File:BCKDHA_Mut219.png|thumb|150px|Figure 5: Hydrogen Bonds for tryptophan on pos 264 in the mutated type structure]]<br />
|}<br />
Although the amino acids cysteine and tryptophan have very different structures and chemical properties, no change in the hydrogen bonding network occurs (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||488.43||87.43<br />
|-<br />
|relative||100%||121%||21%<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||-3745.313620||-1259.860865<br />
|-<br />
|relative|| 100%||66%||34%<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 || 3186.75||2300||-nan||-13603.2<br />
|-<br />
|Angle || 3831.06||370||-nan||-2070.89<br />
|-<br />
|Potential || 3.41e+07||3.3e+07||-nan||-2.03e+08<br />
|}<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|| 3.41e+07||7399900<br />
|-<br />
|relative|| 100%||127%||27%<br />
|}<br />
<br />
The calculated energy for the mutated structure is higher than for the wildtype structure.<br />
<br />
=== Conclusion ===<br />
<br />
return to [[Structure-based_mutation_analysis_BCKDHA| Structure-based mutation analysis]]</div>
Demel