Team:UPO-Sevilla/Project/Improving Flip Flop/Bioinformatics/Tags Finder

From 2011.igem.org

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                             <h1>Tags Finder</h1>
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                             <p><strong>Strategy:</strong> A protein-protein docking has been carried out to obtain an interaction model for the SspB adaptor protein and the protease subunit ClpX. This interaction model would be the first step in the development of a complete real structural model for the degradation process of a target protein by this protease system.</p>
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                             <p><h2>Goal</h2></p>
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<p>To develop a simple Perl program to search a desired tag protein sequence in a query proteome.</p>
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<p><strong>Procedure:</strong></p>  
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<p><h2>Background</h2></p>
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<p>When working with proteases, it is essential to make sure that these proteases are going to degrade only their target proteins, so previous studies must be carried out to get rid of possible unwanted endogenous protease targets. In our case, before starting the web lab experiments, we checked that E.coli’s proteome (our model organism) did not show any of the protease ClpXP degradation tags.</p>
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<li><p>Obtain a pdb model for the SspB and ClpX proteins. In the case of SspB, no pdb model was available for this protein in the <a href="http://www.rcsb.org/pdb/home/home.do">RCSB Protein Data Bank (PDB)</a>, so the protein homology modeling <a href="http://swissmodel.expasy.org/">server Swiss Model</a> and <a href="http://www.cbs.dtu.dk/services/CPHmodels/">CPHmodels 3.0 server</a> were used to obtain a structural model of this protein. However, for ClpX protein several pdb 3D files were available and the largest one was chosen (<a href="http://www.ebi.ac.uk/pdbe-srv/view/entry/3hte/summary.html">PDB entry 3hte</a>).</p></li>
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<p><h2>Strategy</h2></p>  
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<li><p>Run the <a href="http://hex.loria.fr/">Hex</a> protein-protein Docking server. A shape complementarity approach was chosen.</p></li>
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<p>Perl is an open source programming language which is used extensively in Bioinformatics. We wrote a Perl program to search in E.coli’s proteome all the known ClpXP protease degradation tags. By using this software, the user can choose which ClpXP protease known degradation tag wants to search in a desired proteome. The software comes with all the proteomes of the currently used organisms in synthetic biology downloaded from the <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>.</p>
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<li><p>Analyse the docking results. <a href="http://rasmol.org/">RasMol 2.7.5.</a> and <a href="http://jmol.sourceforge.net/">Jmol 12.0</a> molecule viewers were used.</p></li>
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<p><h2>Results</h2></p>
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<p>This software can be downloaded <a href="http://www.upo.es/igem/SearchTagPerl.zip">here</a>.</p>
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Latest revision as of 22:21, 27 October 2011

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Tags Finder

Goal

To develop a simple Perl program to search a desired tag protein sequence in a query proteome.

Background

When working with proteases, it is essential to make sure that these proteases are going to degrade only their target proteins, so previous studies must be carried out to get rid of possible unwanted endogenous protease targets. In our case, before starting the web lab experiments, we checked that E.coli’s proteome (our model organism) did not show any of the protease ClpXP degradation tags.

Strategy

Perl is an open source programming language which is used extensively in Bioinformatics. We wrote a Perl program to search in E.coli’s proteome all the known ClpXP protease degradation tags. By using this software, the user can choose which ClpXP protease known degradation tag wants to search in a desired proteome. The software comes with all the proteomes of the currently used organisms in synthetic biology downloaded from the NCBI.

Results

This software can be downloaded here.

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