Metal-binding Behaviour
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;
<JOBSTART>rhMT1a;
<PDBS>rhMT.pdb;
<BATCH>list1.txt
<COMMANDS>FOLDX_commandfile;
<metalbinding_analysis>rhMT1a,[M];
<MetalBindingEnergy>rhMT1a;
<END>rhMT1a;
<OPTIONS>FOLDX_optionfile;
<Temperature>298;
<R>
<pH>6;
<IonStrength>0.00000125;
<metal>-PREDICT;
<water>-PREDICT;
<num_water_partners>2;
<no_Cterm>false;
<no_Nterm>false;
<OutPDB>true;
<pdb_hydrogens>false;
<pdb_waters>false;
<pdb_hydrogens>false;
<overwriteBatch>false;
<pdb_dummys>false;
<END>rhMT1a;
<JOBEND>rhMT1a;
<ENDFILE>FOLDX_runscript;
Results
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.
</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>
<!--
NewPP limit report
Preprocessor node count: 14/1000000
Post-expand include size: 82/2097152 bytes
Template argument size: 0/2097152 bytes
Expensive parser function count: 0/100
-->
<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 ! HAVE BEEN MOVED HERE -- RDR -->
<div class="visualClear"></div>
<div id='footer-box' class='noprint'>
<div id="footer">
<div id="f-poweredbyico"><a href="https://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="https://creativecommons.org/licenses/by/3.0/"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list">
<!-- Recentchanges is not handles well DEBUG -->
<li id="t-recentchanges"><a href="/Special:RecentChanges"
title='Recent changes'>Recent changes</a></li>
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding"
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li>
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding"
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li>
<li id="t-specialpages"><a href="/Special:SpecialPages"
title="List of all special pages [q]" accesskey="q">Special pages</a>
</li>
<li><a href='/Special:Preferences'>My preferences</a></li>
</ul>
</div> <!-- close footer -->
<div id='footer'>
<ul id="f-list">
<li id="t-print"><a href="/wiki/index.php?title=Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding&direction=prev&oldid=236989&printable=yes"
title="Printable version of this page [p]" accesskey="p">Printable version</a>
</li>
<li id="t-permalink"><a href="/wiki/index.php?title=Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding&oldid=236773"
title="Permanent link to this revision of the page">Permanent link</a>
</li>
<li id="privacy"><a href="/2012.igem.org:Privacy_policy" title="2012.igem.org:Privacy policy">Privacy policy</a></li>
<li id="disclaimer"><a href="/2012.igem.org:General_disclaimer" title="2012.igem.org:General disclaimer">Disclaimers</a></li>
</ul>
</div> <!-- close footer -->
</div> <!-- close footer-box -->
<script>if (window.runOnloadHook) runOnloadHook();</script>
</div>
<!-- Served in 0.153 secs. --></body>
</html>
"