http://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&feed=atom&action=historyTeam:EPF-Lausanne/Results - Revision history2024-03-28T19:09:05ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159373&oldid=prevNbranden at 23:20, 21 October 20092009-10-21T23:20:59Z<p></p>
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</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159358&oldid=prevNbranden: /* L453G */2009-10-21T23:20:29Z<p><span class="autocomment">L453G</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><center><big><font color="red"><b><i>Click on each title below to access the results.</i></b></font></big></center></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><center><big><font color="red"><b><i>Click on each title below to access the <ins class="diffchange diffchange-inline">detailled </ins>results.</i></b></font></big></center></div></td></tr>
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</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159345&oldid=prevNbranden: /* L453G */2009-10-21T23:19:59Z<p><span class="autocomment">L453G</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><big><font color="red"><b><i>Click on each title below to access the results.</i></b></font></big></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><center></ins><big><font color="red"><b><i>Click on each title below to access the results.</i></b></font></big<ins class="diffchange diffchange-inline">></center</ins>></div></td></tr>
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</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159311&oldid=prevNbranden: /* Simulations of non-light activated LOV2 domain with specific mutations */2009-10-21T23:19:06Z<p><span class="autocomment">Simulations of non-light activated LOV2 domain with specific mutations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This mutation gave very interesting results: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This mutation gave very interesting results: </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:<<del class="diffchange diffchange-inline">b</del>><big>It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~57% in the I427F mutant.</big></<del class="diffchange diffchange-inline">b</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:<<ins class="diffchange diffchange-inline">i</ins>><big>It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~57% in the I427F mutant.</big></<ins class="diffchange diffchange-inline">i</ins>></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*Important result, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#ILE427_to_PHE here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*Important result, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#ILE427_to_PHE here]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>So, an <<del class="diffchange diffchange-inline">b</del>>important hypothesis</<del class="diffchange diffchange-inline">b</del>> appears:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>So, an <<ins class="diffchange diffchange-inline">i</ins>>important hypothesis</<ins class="diffchange diffchange-inline">i</ins>> appears:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:If the cystein's side chain points more often toward its reacting carbon in the FMN, there is more chances that upon light activation a covalent bond will be made. Moreover, if there is more steric obstruction toward the unbonding this newly formed covalent bond, this covalent bond will be stabilized, and it will finally leads to a general stabilization of the light activated state of the protein.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:If the cystein's side chain points more often toward its reacting carbon in the FMN, there is more chances that upon light activation a covalent bond will be made. Moreover, if there is more steric obstruction toward the unbonding this newly formed covalent bond, this covalent bond will be stabilized, and it will finally leads to a general stabilization of the light activated state of the protein.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This mutation gave less interesting results than the first mutation: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This mutation gave less interesting results than the first mutation: </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:<<del class="diffchange diffchange-inline">b</del>>It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~31% in the I427F mutant.</<del class="diffchange diffchange-inline">b</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:<<ins class="diffchange diffchange-inline">i</ins>>It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~31% in the I427F mutant.</<ins class="diffchange diffchange-inline">i</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*Important result, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#LEU453_to_GLY here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*Important result, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#LEU453_to_GLY here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>So, an <<del class="diffchange diffchange-inline">b</del>>important hypothesis</<del class="diffchange diffchange-inline">b</del>> appears:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>So, an <<ins class="diffchange diffchange-inline">i</ins>>important hypothesis</<ins class="diffchange diffchange-inline">i</ins>> appears:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.</div></td></tr>
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</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159253&oldid=prevNbranden: /* Wild type simulations */2009-10-21T23:17:29Z<p><span class="autocomment">Wild type simulations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"># </del><i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:1. </ins><i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"># </del><i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:2. </ins><i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"># </del>The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:3. </ins>The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"># </del>Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">:4. </ins>Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td></tr>
</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159228&oldid=prevNbranden: /* Wild type simulations */2009-10-21T23:16:49Z<p><span class="autocomment">Wild type simulations</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<td colspan='2' style="background-color: white; color:black;">Revision as of 23:16, 21 October 2009</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">:</del># <i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># <i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">:</del># <i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># <i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">:</del># The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">:</del># Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td></tr>
</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159209&oldid=prevNbranden: /* Wild type simulations */2009-10-21T23:16:14Z<p><span class="autocomment">Wild type simulations</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<td colspan='2' style="background-color: white; color:black;">Revision as of 23:16, 21 October 2009</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 71:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:<del class="diffchange diffchange-inline">- </del><i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:<ins class="diffchange diffchange-inline"># </ins><i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:<del class="diffchange diffchange-inline">- </del><i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:<ins class="diffchange diffchange-inline"># </ins><i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:<del class="diffchange diffchange-inline">- </del>The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:<ins class="diffchange diffchange-inline"># </ins>The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:<del class="diffchange diffchange-inline">- </del>Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:<ins class="diffchange diffchange-inline"># </ins>Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td></tr>
</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159191&oldid=prevNbranden: /* Wild type simulations */2009-10-21T23:15:34Z<p><span class="autocomment">Wild type simulations</span></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=<font color="#007CBC"><big> Summary of the main results </big></font>=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=<font color="#007CBC"><big> Summary of the main results </big></font>=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<font color="#007CBC"> Wild type simulations </font>==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<font color="#007CBC"> Wild type simulations </font>==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>First of all, the <<del class="diffchange diffchange-inline">b</del>>equilibration</<del class="diffchange diffchange-inline">b</del>> (stabilization of temperature, pressure and density) was accurate for both states of LOV2 domain. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>First of all, the <<ins class="diffchange diffchange-inline">i</ins>>equilibration</<ins class="diffchange diffchange-inline">i</ins>> (stabilization of temperature, pressure and density) was accurate for both states of LOV2 domain. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/EDS#Evolution_of_Pression.2C_Volume_and_Temperature here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/EDS#Evolution_of_Pression.2C_Volume_and_Temperature here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Secondly, we analyzed many important characteristics of the system: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:- <<del class="diffchange diffchange-inline">b</del>>RMSD</<del class="diffchange diffchange-inline">b</del>> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:- <<ins class="diffchange diffchange-inline">i</ins>>RMSD</<ins class="diffchange diffchange-inline">i</ins>> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 77:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:- <<del class="diffchange diffchange-inline">b</del>>RMSF</<del class="diffchange diffchange-inline">b</del>> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:- <<ins class="diffchange diffchange-inline">i</ins>>RMSF</<ins class="diffchange diffchange-inline">i</ins>> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:- The <<del class="diffchange diffchange-inline">b</del>>angle between the main beta sheet and the J-alpha helix</<del class="diffchange diffchange-inline">b</del>> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:- The <<ins class="diffchange diffchange-inline">i</ins>>angle between the main beta sheet and the J-alpha helix</<ins class="diffchange diffchange-inline">i</ins>> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:- Side chain <<del class="diffchange diffchange-inline">b</del>>dihedral angle</<del class="diffchange diffchange-inline">b</del>> of the reactive cystein (residue 450) was computed for both state.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:- Side chain <<ins class="diffchange diffchange-inline">i</ins>>dihedral angle</<ins class="diffchange diffchange-inline">i</ins>> of the reactive cystein (residue 450) was computed for both state.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.</div></td></tr>
</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159160&oldid=prevNbranden at 23:14, 21 October 20092009-10-21T23:14:37Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=<font color="#007CBC"><big> Summary of the main results </big></font>=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=<font color="#007CBC"><big> Summary of the main results </big></font>=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<font color="#007CBC"> Wild type simulations </font>==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==<font color="#007CBC"> Wild type simulations </font>==</div></td></tr>
</table>Nbrandenhttp://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results&diff=159135&oldid=prevNbranden at 23:13, 21 October 20092009-10-21T23:13:54Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>So, an <b>important hypothesis</b> appears:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>So, an <b>important hypothesis</b> appears:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td></tr>
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