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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<br>
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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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<br>
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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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<table class="image" align="center">
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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.
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<caption align="bottom">.</caption>
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<tr><td><img src="https://static.igem.org/mediawiki/2012/1/16/UANLDCSelection_006.png" style="width:300px;"></td></tr>
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</table>
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<br>
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<p><b>Results</b></p>
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<br>
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<p>The algorithm described above 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>
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<br>
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<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"><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/structure_prediction"><li>Structure Prediction</a></li>
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<a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/assemblies_stability"><li>Assemblies Stability</a></li>
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<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/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>
<a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/references"><li>References</a></li>

Latest revision as of 03:51, 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.


.

Results


The algorithm described above 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.


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