Team:UANL Mty-Mexico/Modeling/3Dmodel/Metal-binding

From 2012.igem.org

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<p><br><h3>Metal-binding Behaviour</h3></p>
<p><br><h3>Metal-binding Behaviour</h3></p>
<br>
<br>
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Metal-binding behaviour
 
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Methodology
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<p><b>Methodology</b></p>
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We used the FoldX force field (Schymkowitz et al. 2005) to predict the metal-binding sites and energies of the predicted partial tertiary structure of rhM. The ionic strength, and pH were adjusted in order to simulate the experimental conditions, we tested the following algorithm replacing the field [M] (6th line) with the  atoms Ca, Mg, Mn, Na, Zn, Fe, Cu, Co, K, also considering the changes in the ionic strength.
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<TITLE>FOLDX_runscript;
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<p>We used the FoldX force field (Schymkowitz et al. 2005) to predict the metal-binding sites and energies of the predicted partial tertiary structure of rhM. The ionic strength, and pH were adjusted in order to simulate the experimental conditions, we tested the following algorithm replacing the field [M] (6th line) with the  atoms Ca, Mg, Mn, Na, Zn, Fe, Cu, Co, K, also considering the changes in the ionic strength.</p>
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<JOBSTART>rhMT1a;
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<PDBS>rhMT.pdb;
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<BATCH>list1.txt
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<COMMANDS>FOLDX_commandfile;
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<metalbinding_analysis>rhMT1a,[M];
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<MetalBindingEnergy>rhMT1a;
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<END>rhMT1a;
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<OPTIONS>FOLDX_optionfile;
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<Temperature>298;
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<R>
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<pH>6;
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<IonStrength>0.00000125;
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<metal>-PREDICT;
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<water>-PREDICT;
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<num_water_partners>2;
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<no_Cterm>false;
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<no_Nterm>false;
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<OutPDB>true;
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<pdb_hydrogens>false;
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<pdb_waters>false;
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<pdb_hydrogens>false;
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<overwriteBatch>false;
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<pdb_dummys>false;
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<END>rhMT1a;
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<JOBEND>rhMT1a;
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<ENDFILE>FOLDX_runscript;
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Results
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<p><TITLE>FOLDX_runscript;</p>
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The algorithm described below did not predict any metal-binding site. Presumably due to the lack of “precision” of the partial model. We expect to obtain metalbinding sites by obtaining more accurate models of rhMT.
+
<p><JOBSTART>rhMT1a;</p>
 +
<p><PDBS>rhMT.pdb;</p>
 +
<p><BATCH>list1.txt</p>
 +
<p><COMMANDS>FOLDX_commandfile;</p>
 +
<p><metalbinding_analysis>rhMT1a,[M];</p>
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<p><MetalBindingEnergy>rhMT1a;</p>
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<p><END>rhMT1a;</p>
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<p><OPTIONS>FOLDX_optionfile;</p>
 +
<p><Temperature>298;</p>
 +
<p><R></p>
 +
<p><pH>6;</p>
 +
<p><IonStrength>0.00000125;</p>
 +
<p><metal>-PREDICT;</p>
 +
<p><water>-PREDICT;</p>
 +
<p><num_water_partners>2;</p>
 +
<p><no_Cterm>false;</p>
 +
<p><no_Nterm>false;</p>
 +
<p><OutPDB>true;</p>
 +
<p><pdb_hydrogens>false;</p>
 +
<p><pdb_waters>false;</p>
 +
<p><pdb_hydrogens>false;</p>
 +
<p><overwriteBatch>false;</p>
 +
<p><pdb_dummys>false;</p>
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<p><END>rhMT1a;</p>
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<p><JOBEND>rhMT1a;</p>
 +
<p><ENDFILE>FOLDX_runscript;</p>
 +
 
 +
<p><b>Results</b></p>
 +
 
 +
<p>The algorithm described below did not predict any metal-binding site. Presumably due to the lack of “precision” of the partial model. We expect to obtain metalbinding sites by obtaining more accurate models of rhMT.</p>

Revision as of 03:36, 27 September 2012

iGEM UANL 2012


Metal-binding Behaviour


Methodology

We used the FoldX force field (Schymkowitz et al. 2005) to predict the metal-binding sites and energies of the predicted partial tertiary structure of rhM. The ionic strength, and pH were adjusted in order to simulate the experimental conditions, we tested the following algorithm replacing the field [M] (6th line) with the atoms Ca, Mg, Mn, Na, Zn, Fe, Cu, Co, K, also considering the changes in the ionic strength.

FOLDX_runscript;</p> <p><JOBSTART>rhMT1a;</p> <p><PDBS>rhMT.pdb;</p> <p><BATCH>list1.txt</p> <p><COMMANDS>FOLDX_commandfile;</p> <p><metalbinding_analysis>rhMT1a,[M];</p> <p><MetalBindingEnergy>rhMT1a;</p> <p><END>rhMT1a;</p> <p><OPTIONS>FOLDX_optionfile;</p> <p><Temperature>298;</p> <p><R></p> <p><pH>6;</p> <p><IonStrength>0.00000125;</p> <p><metal>-PREDICT;</p> <p><water>-PREDICT;</p> <p><num_water_partners>2;</p> <p><no_Cterm>false;</p> <p><no_Nterm>false;</p> <p><OutPDB>true;</p> <p><pdb_hydrogens>false;</p> <p><pdb_waters>false;</p> <p><pdb_hydrogens>false;</p> <p><overwriteBatch>false;</p> <p><pdb_dummys>false;</p> <p><END>rhMT1a;</p> <p><JOBEND>rhMT1a;</p> <p><ENDFILE>FOLDX_runscript;</p> <p><b>Results</b></p> <p>The algorithm described below did not predict any metal-binding site. Presumably due to the lack of “precision” of the partial model. We expect to obtain metalbinding sites by obtaining more accurate models of rhMT.</p> </div> <div class="sidebar2"> <ul class="nav"> <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel"><li>Overview</a></li> <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/structure_prediction"><li>Structure Prediction</a></li> <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/assemblies_stability"><li>Assemblies Stability</a></li> <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding"><li><b>>>Metal-binding Behaviour</b></a></li> <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/references"><li>References</a></li> </ul> </div> </p><p> <body> <div class="footer"> <!--Share--> <!-- AddThis Button BEGIN --> <div class="addthis_toolbox addthis_default_style "> <a class="addthis_button_preferred_1"></a> <a class="addthis_button_preferred_2"></a> <a class="addthis_button_preferred_3"></a> <a class="addthis_button_preferred_4"></a> <a class="addthis_button_compact"></a> <a class="addthis_counter addthis_bubble_style"></a> </div> <script type="text/javascript" src="http://s7.addthis.com/js/250/addthis_widget.js#pubid=xa-504e81c2782b3893"></script> <!-- AddThis Button END --> <!-- end .footer --></div> <!-- logo --> <div class="content"> <p><a href="https://igem.org/Main_Page"><span style="position:absolute; top:-90px; left:810px; width: 147px; height: 154px;"><img src="https://static.igem.org/mediawiki/2012/b/bc/UANL2012logo.png" width="183" height="196" alt="logo" /></span></a></p> </div> </div> </body> </p><div class="printfooter"> Retrieved from "<a href="http://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding">http://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding</a>"</div> <div id="catlinks"><div id='catlinks' class='catlinks catlinks-allhidden'></div></div> <!-- end content --> <div class="visualClear"></div> </div> </div> <!-- PAGE FOOTER -- ITEMS FROM COLUMN ! 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