Team:Goettingen/project overview/project drylab

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<div class="proRP" id="rpart1">
<div class="proRP" id="rpart1">
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        <div class="trans_zh"><a href="https://2014.igem.org/Team:Goettingen/project_overview/project_drylab_ZH"><b>中文</b></a></div>
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       <div id="goenext"><a href="https://2014.igem.org/Team:Goettingen/project_overview/perspectives"><img src='https://static.igem.org/mediawiki/2014/3/32/Goettingen2014-previous.png' width='40px'></a> 9/15 <a href="https://2014.igem.org/Team:Goettingen/project_overview/project_wetlab"><img src='https://static.igem.org/mediawiki/2014/e/ea/Goettingen2014-next.png' width='40px'></a></div><br /><br /><br />
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       <h1>Dry lab</h1>
-
      <h1><center><b>Dry lab</b></center></h1>
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       <h2 id="approach">Homology modelling</h2>
-
<br /><br />
+
       <p>We modeled the 3D structure of our peptide-containing scaffolds (domain B1 of protein G from <i>Staphylococcus aureus</i>) by homology modelling. We used the <a href="http://salilab.org/modeller/" target="1">Modeller library</a> to accomplish that; since the peptide is about 20-25 amino acids long, it can be modeled as a loop inside the B1 domain scaffold for which there are already a number of 3D structures available at the Protein Data Bank.</p>
-
       <h2><font color = "green"><center><b>Homology modelling</b></center></font></h2>
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-
       <p>We modeled the 3D structure of our peptide-containing scaffolds (domain B1 of protein G from <i>Staphylococcus aureus</i>) by homology modelling. We used <a href="https://salilab.org/modeller/" target="1">Modeller library</a> to accomplish that; since the peptide is about 20-25 amino acid residues long, it can be modeled as a loop inside the B1 domain scaffold for which there are already a number of 3D structures available at the Protein Data Bank.</p>
+
       <br />
       <br />
-
<a href="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" target="1"><img src="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" width="700" /></a><center><figure><figcaption>Homology modeling procedure. All peptides were cloned inside a scaffold (B1 domain of protein G from <i>Streptococcus aureus</i>. The peptides were short enough to be modeled as an internal loop by loop refinement; however, these structures should only be considered as a working model, since we don't have direct crystallographic data.</figcaption></figure></center><br /><br />
+
<a href="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" target="1"><img src="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" width="700" /></a><center><br /><p align = "justify">This is the general homology modeling procedure we followed. All peptides were cloned inside a scaffold (B1 domain of protein G from <i>Staphylococcus aureus</i>. The peptides were short enough to be modeled as an internal loop by loop refinement; these structures should only be considered as a working model, since we do not have direct crystallographic data. <a href="https://2014.igem.org/Team:Goettingen/notebook_drylab">A detailed procedure can be found in this link.</a></p></center><br /><br />
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<hr>
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-
<br /><br />
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<h2><font color = "green"><center><b>References</b></center></font></h2>
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<br /><h2 id="dlresults">Results summary</h2>
 +
<h3>Protein G scaffold</h3>
 +
<p>The following table is a summary of the models we generated for our peptides inside the protein G scaffold. Their main purpose is to give us an idea if the calculated energy profile matches our assumption that the peptide is being exposed to the exterior of the scaffold. These models are in no way definitive, since we lack direct crystalographic data. </p><br />
 +
 
 +
 +
<center><table class="table1" style="width:700px">
 +
<tr style="font-weight:bold;">
 +
<th style="font-size:80%;">Peptide</th>
 +
<th style="font-size:80%;">PNG*</th>
 +
<th style="font-size:80%;">PDB</th>
 +
<th style="font-size:80%;">Peptide location</th>
 +
<th style="font-size:80%;">QMEAN score</th>
 +
<th style="font-size:80%;">Overall DOPE score</th>
 +
<th style="font-size:80%;">Energy profile</th>
 +
</tr>
 +
 
 +
<tr>
 +
<td style="font-size:80%;">Prey 3</td>
 +
<td style="font-size:80%;">
 +
<!--
 +
<video width="120px" controls><source src="https://static.igem.org/mediawiki/2014/6/67/Goettingen_Prey_3a.mov" type="video/mov"> Your browser does not support HTML5 video.</video>
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<a href="https://static.igem.org/mediawiki/2014/6/62/Goettingen-Prey3.png" target="1"><img src="https://static.igem.org/mediawiki/2014/6/62/Goettingen-Prey3.png" width=100></a>
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 +
</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/1/1e/Goettingen-Prey3-input.txt" target="1">Download</a></td>
 +
 
 +
<td style="font-size:80%;">K17-E42</td>
 +
<td style="font-size:70%;">0.512</td>
 +
<td style="font-size:70%;">-7053.966797</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/3/37/GoettingenPrey3-profile.txt" target="1">Download</a></td>
 +
</tr>
 +
 
 +
<tr>
 +
<td style="font-size:80%;">Prey 4.1</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/6/6e/Goettingen-Prey4-1.png" target="1"><img src="https://static.igem.org/mediawiki/2014/6/6e/Goettingen-Prey4-1.png" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/1/1b/Goettingen-Prey4-1.txt" target="1">Download</a></td>
 +
 
 +
<td style="font-size:80%;">K17-E44</td>
 +
<td style="font-size:70%;">0.468</td>
 +
<td style="font-size:70%;">-7246.956055</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/0/0b/GoettingenPrey4-1-profile.txt" target="1">Download</a></td>
 +
</tr>
 +
 
 +
<tr>
 +
<td style="font-size:80%;">Prey 5</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/4/4e/Goettingen-Prey5.png" target="1"><img src="https://static.igem.org/mediawiki/2014/4/4e/Goettingen-Prey5.png" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/8/86/Goettingen-Prey5.txt" target="1">Download</a></td>
 +
 
 +
<td style="font-size:80%;">K17-E44</td>
 +
<td style="font-size:70%;">0.495</td>
 +
<td style="font-size:70%;">-7501.071777</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/1/10/GoettingenPrey5-profile.txt" target="1">Download</a></td>
 +
</tr>
 +
 
 +
 
 +
 
 +
<tr>
 +
<td style="font-size:80%;">Prey 13</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/1/1c/Prey13.png" target="1"><img src="https://static.igem.org/mediawiki/2014/1/1c/Prey13.png" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Prey13-input.txt" target="1">Download</a></td>
 +
 
 +
<td style="font-size:80%;>">K17-E42</td>
 +
<td style="font-size:70%;">0.535</td>
 +
<td style="font-size:70%;">-7729.056152</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/e/eb/GoettingenPrey13-profile.txt" target="1">Download</a></td>
 +
</tr>
 +
 
 +
<tr>
 +
<td style="font-size:80%;">Prey 15</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/4/41/Prey15.png"><img src="https://static.igem.org/mediawiki/2014/4/41/Prey15.png" target="1" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/7/77/Goettingen-Prey15-input.txt" target="1">Download</a></td>
 +
 
 +
<td style="font-size:80%;">K17-E42</td>
 +
<td style="font-size:70%;">0.441</td>
 +
<td style="font-size:70%;">-7685.998535</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/2/20/GoettingenPrey15-profile.txt" target="1">Download</a></td>
 +
</tr>
 +
</table></center><p style="font-size:10px"><b>*The peptide is shown in red and the scaffold in blue.</b></p>
<br />
<br />
-
<ol>
 
-
<li>1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan,
 
-
D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure
 
-
Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley
 
-
&amp; Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.</li><br />
 
-
<li>2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez,
+
<h3>GFP scaffold</h3>
-
F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes.
+
<p>These are the structures we generated for our peptides inside a GFP scaffold.</p><br />
-
Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.</li><br />
+
-
<li>3. A. Sali &amp; T.L. Blundell.
+
-
Comparative protein modelling by satisfaction of spatial restraints. J.
+
<center><table class="table1" style="width:700px">
-
Mol. Biol. 234, 779-815, 1993.</li><br />
+
<tr style="font-weight:bold;">
-
<li>4. A. Fiser, R.K. Do, &amp; A. Sali.
+
<th style="font-size:80%;">Peptide</th>
-
Modeling of loops in protein structures, Protein Science 9. 1753-1773,
+
<th style="font-size:80%;">PNG*</th>
-
2000.</li><br />
+
<th style="font-size:80%;">PDB</th>
-
</ol>
+
<th style="font-size:80%;">Peptide location</th>
-
      <div id="goenext"><a href="https://2014.igem.org/Team:Goettingen/project_overview/perspectives"><img src='https://static.igem.org/mediawiki/2014/3/32/Goettingen2014-previous.png' width='40px'></a> 9/15 <a href="https://2014.igem.org/Team:Goettingen/project_overview/project_wetlab"><img src='https://static.igem.org/mediawiki/2014/e/ea/Goettingen2014-next.png' width='40px'></a></div><br />
+
<th style="font-size:80%;">QMEAN score</th>
 +
<th style="font-size:80%;">Overall DOPE score</th>
 +
<th style="font-size:80%;">Energy profile</th>
 +
</tr>
-
<!-- end of right column-->
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<tr>
-
<div class="fb-like" data-layout="standard" data-action="like" data-show-faces="true" data-share="true"></div>
+
<td style="font-size:80%;">Prey 3</td>
-
<script>
+
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/f/f5/GfpPrey3.png" target="1"><img src="https://static.igem.org/mediawiki/2014/f/f5/GfpPrey3.png" width=100></a></td>
-
var curl = document.URL;
+
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/8/8c/Prey3-gfp.pdb.txt" target="1">Download</a></td>
-
$( '#fb-like' ).attr('data-href', curl);
+
 +
<td style="font-size:80%;">E103-E127</td>
 +
<td style="font-size:70%;">0.43</td>
 +
<td style="font-size:70%;">-26798.28125</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/4/4a/Prey3-gfp.pdb.profile.txt" target="1">Download</a></td>
 +
</tr>
-
</script>
+
<tr>
 +
<td style="font-size:80%;">Prey 4.1</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/6/62/GfpPrey4.png" target="1"><img src="https://static.igem.org/mediawiki/2014/6/62/GfpPrey4.png" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/8/89/Prey4-gfp.pdb.txt" target="1">Download</a></td>
-
</div>
+
<td style="font-size:80%;">E103-E127</td>
 +
<td style="font-size:70%;">0.448</td>
 +
<td style="font-size:70%;">-27891.212891</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/d/dd/GFP-aSsr1.pdb.profile.txt" target="1">Download</a></td>
 +
</tr>
 +
<tr>
 +
<td style="font-size:80%;">Prey 5</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/a/a7/GfpPrey5.png" target="1"><img src="https://static.igem.org/mediawiki/2014/a/a7/GfpPrey5.png" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/b/bc/Prey5-gfp.pdb.txt" target="1">Download</a></td>
-
</div>
+
<td style="font-size:80%;">E103-E127</td>
-
</div>
+
<td style="font-size:70%;">0.483</td>
 +
<td style="font-size:70%;">-26633.4375</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/3/3c/Prey5-gfp.pdb.profile.txt" target="1">Download</a></td>
 +
</tr>
-
<script>$(document).keydown(function(e) {
 
-
    switch(e.which) {
 
-
        case 37: // left
 
-
window.location = url8;
+
<tr>
-
break;
+
<td style="font-size:80%;">Prey 13</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/f/f3/GfpPrey13.png" target="1"><img src="https://static.igem.org/mediawiki/2014/f/f3/GfpPrey13.png" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/0/09/Prey13-gfp.pdb.txt" target="1">Download</a></td>
-
        case 39: // right
+
<td style="font-size:80%;>">E103-E127</td>
 +
<td style="font-size:70%;">0.404</td>
 +
<td style="font-size:70%;">-27075.160156</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/a/a6/Prey13-gfp.pdb.profile.txt" target="1">Download</a></td>
 +
</tr>
-
window.location = url10;
+
<tr>
-
        break;
+
<td style="font-size:80%;">Prey 15</td>
 +
<td style="font-size:80%;"><a href="https://static.igem.org/mediawiki/2014/f/f7/GfpPrey15.png"><img src="https://static.igem.org/mediawiki/2014/f/f7/GfpPrey15.png" target="1" width=100></a></td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/e/ed/Prey15-gfp.pdb.txt" target="1">Download</a></td>
-
     
+
<td style="font-size:80%;">E103-E127</td>
 +
<td style="font-size:70%;">0.413</td>
 +
<td style="font-size:70%;">-26713.355469</td>
 +
<td style="font-size:70%;"><a href="https://static.igem.org/mediawiki/2014/0/00/Prey15-gfp.pdb.profile.txt" target="1">Download</a></td>
 +
</tr>
 +
</table></center><p style="font-size:10px"><b>*The peptide is shown in red and the scaffold in green.</b></p>
 +
<br />
 +
 
 +
 
 +
 
 +
<br />
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<hr>
 +
<h2>References</h2>
 +
<br />
 +
<ol>
 +
<li><p>1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan,
 +
D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure
 +
Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley
 +
&amp; Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.</p></li><br />
 +
 
 +
<li><p>2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez,
 +
F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes.
 +
Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.</p></li><br />
 +
 
 +
<li><p>3. A. Sali &amp; T.L. Blundell.
 +
Comparative protein modelling by satisfaction of spatial restraints. J.
 +
Mol. Biol. 234, 779-815, 1993.</p></li><br />
 +
<li><p>4. A. Fiser, R.K. Do, &amp; A. Sali.
 +
Modeling of loops in protein structures, Protein Science 9. 1753-1773,
 +
2000.</p></li><br />
 +
</ol>
 +
<div><a href="https://2014.igem.org/Team:Goettingen/project_overview/project_wetlab" class="button_pre"><b>Previous</b></a><a href="https://2014.igem.org/Team:Goettingen/project_overview/perspectives" class="button_next"><b>Next</b></a></div>
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Latest revision as of 12:51, 17 October 2014

Project

中文

Dry lab

Homology modelling

We modeled the 3D structure of our peptide-containing scaffolds (domain B1 of protein G from Staphylococcus aureus) by homology modelling. We used the Modeller library to accomplish that; since the peptide is about 20-25 amino acids long, it can be modeled as a loop inside the B1 domain scaffold for which there are already a number of 3D structures available at the Protein Data Bank.



This is the general homology modeling procedure we followed. All peptides were cloned inside a scaffold (B1 domain of protein G from Staphylococcus aureus. The peptides were short enough to be modeled as an internal loop by loop refinement; these structures should only be considered as a working model, since we do not have direct crystallographic data. A detailed procedure can be found in this link.




Results summary

Protein G scaffold

The following table is a summary of the models we generated for our peptides inside the protein G scaffold. Their main purpose is to give us an idea if the calculated energy profile matches our assumption that the peptide is being exposed to the exterior of the scaffold. These models are in no way definitive, since we lack direct crystalographic data.


Peptide PNG* PDB Peptide location QMEAN score Overall DOPE score Energy profile
Prey 3 Download K17-E42 0.512 -7053.966797 Download
Prey 4.1 Download K17-E44 0.468 -7246.956055 Download
Prey 5 Download K17-E44 0.495 -7501.071777 Download
Prey 13 Download K17-E42 0.535 -7729.056152 Download
Prey 15 Download K17-E42 0.441 -7685.998535 Download

*The peptide is shown in red and the scaffold in blue.


GFP scaffold

These are the structures we generated for our peptides inside a GFP scaffold.


Peptide PNG* PDB Peptide location QMEAN score Overall DOPE score Energy profile
Prey 3 Download E103-E127 0.43 -26798.28125 Download
Prey 4.1 Download E103-E127 0.448 -27891.212891 Download
Prey 5 Download E103-E127 0.483 -26633.4375 Download
Prey 13 Download E103-E127 0.404 -27075.160156 Download
Prey 15 Download E103-E127 0.413 -26713.355469 Download

*The peptide is shown in red and the scaffold in green.



References


  1. 1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.


  2. 2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.


  3. 3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.


  4. 4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.





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