Difference between revisions of "Team:Aix-Marseille/Modeling"
(34 intermediate revisions by 3 users not shown) | |||
Line 4: | Line 4: | ||
<meta name="viewport" content="width=device-width, initial-scale=1.0"> | <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
<meta http-equiv="content-type" content="text/html; charset=UTF-8"> | <meta http-equiv="content-type" content="text/html; charset=UTF-8"> | ||
− | <link rel="stylesheet" href="https://2015.igem.org/Team: | + | <link rel="stylesheet" href="https://2015.igem.org/Team:NRP-UEA-Norwich/bootstrapcss?action=raw&ctype=text/css" type="text/css"> |
− | <link rel="stylesheet" href="https://2015.igem.org/Team: | + | <link rel="stylesheet" href="https://2015.igem.org/Team:NRP-UEA-Norwich/mobilecss?action=raw&ctype=text/css" type="text/css"> |
− | <script type="text/javascript" src="https://2015.igem.org/Team: | + | <script type="text/javascript" src="https://2015.igem.org/Team:NRP-UEA-Norwich/bootstrap.js?action=raw&ctype=text/javascript"></script> |
<!--[if lt IE 7]> | <!--[if lt IE 7]> | ||
Line 33: | Line 33: | ||
color: #FFFFFF !important; | color: #FFFFFF !important; | ||
} .bg-1 { | } .bg-1 { | ||
− | background: url( | + | background: url(https://static.igem.org/mediawiki/2015/f/f3/FrsJhjG.jpg);background-repeat:no-repeat; |
background-size:cover; | background-size:cover; | ||
min-height: 600px; | min-height: 600px; | ||
Line 64: | Line 64: | ||
</button> | </button> | ||
− | <a href="/Team:Aix Marseille" class="navbar-brand hidden-lg hidden-md hidden-sm" >< | + | <a href="/Team:Aix Marseille" class="navbar-brand hidden-lg hidden-md hidden-sm" ><https://static.igem.org/mediawiki/2015/6/6e/OHSATfM.png" class="img-responsive" width="80" height="80"></a> |
</div> | </div> | ||
Line 71: | Line 71: | ||
<div class="collapse navbar-collapse " id="bs-example-navbar-collapse-1"> | <div class="collapse navbar-collapse " id="bs-example-navbar-collapse-1"> | ||
<ul class="nav navbar-nav " id="nav"> | <ul class="nav navbar-nav " id="nav"> | ||
− | <li><a href="/Team:Aix-Marseille" class="logo"><img src=" | + | <li><a href="/Team:Aix-Marseille" class="logo"><img src="https://static.igem.org/mediawiki/2015/6/6e/OHSATfM.png" class="img-responsive" width="85" height="85"></a></li> |
<li ><a href="/Team:Aix-Marseille">Home</a></li> | <li ><a href="/Team:Aix-Marseille">Home</a></li> | ||
<li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown">Project</a> | <li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown">Project</a> | ||
<ul class="dropdown-menu"> | <ul class="dropdown-menu"> | ||
− | <li ><a href="/Team:Aix-Marseille/Project/Description"> | + | <li ><a href="/Team:Aix-Marseille/Project/Description">Overview</a></li> |
<li ><a href="/Team:Aix-Marseille/Design">Project design</a></li> | <li ><a href="/Team:Aix-Marseille/Design">Project design</a></li> | ||
<li ><a href="/Team:Aix-Marseille/Parts">Parts</a></li> | <li ><a href="/Team:Aix-Marseille/Parts">Parts</a></li> | ||
Line 97: | Line 97: | ||
<li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown">Interlab Study</a> | <li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown">Interlab Study</a> | ||
<ul class="dropdown-menu"> | <ul class="dropdown-menu"> | ||
+ | <li ><a href="/Team:Aix-Marseille/Notebook2">Calendar</a></li> | ||
<li ><a href="/Team:Aix-Marseille/Measurement">Results</a></li> | <li ><a href="/Team:Aix-Marseille/Measurement">Results</a></li> | ||
− | <li ><a href="/Team:Aix-Marseille/Protocols2"> | + | <li ><a href="/Team:Aix-Marseille/Protocols2">Protocols</a></li> |
<li ><a href="/Team:Aix-Marseille/Sequencing/data">Sequencing data</a></li> | <li ><a href="/Team:Aix-Marseille/Sequencing/data">Sequencing data</a></li> | ||
</ul> | </ul> | ||
Line 107: | Line 108: | ||
</ul> | </ul> | ||
</li> | </li> | ||
− | + | <li class="dropdown " id="dropdown"><a href="/Team:Aix-Marseille/Achievement" class="dropdown-toggle" data-toggle="dropdown">Achievement</a></li> | |
</li> | </li> | ||
Line 140: | Line 141: | ||
<p class="space20"><div align="justify"><span style="font-family:Courier New">We are delighted to present our models and hope that they will seem clear and explicit. | <p class="space20"><div align="justify"><span style="font-family:Courier New">We are delighted to present our models and hope that they will seem clear and explicit. | ||
During our project, we have expressed several enzymes and built several systems. Therefore, we needed enzymatic models and computer simulation to assess their effectiveness, their stability, and improved them. | During our project, we have expressed several enzymes and built several systems. Therefore, we needed enzymatic models and computer simulation to assess their effectiveness, their stability, and improved them. | ||
− | We initially chose 3 laccases (B.subtilis, E.coli, T.thermophilus) and 3 cytochromes C (Shewanella oneidensis, Synechocystis sp, Paracoccus denitrificans). | + | We initially chose 3 laccases (<i>B.subtilis</i>, <i>E.coli</i>, <i>T.thermophilus</i>) and 3 cytochromes C (<i>Shewanella oneidensis</i>, <i>Synechocystis sp</i>, <i>Paracoccus denitrificans</i>). |
The purpose of our simulations was to determine a custom linker for each of our constructions. | The purpose of our simulations was to determine a custom linker for each of our constructions. | ||
The challenge was to increase the chances of contact between the two enzymes to allow electron transfer. So we had to simulate a system in which our enzymes are pre-positioned. It also involved the selection of a structured linker (alpha helix) to maintain proper conformation. | The challenge was to increase the chances of contact between the two enzymes to allow electron transfer. So we had to simulate a system in which our enzymes are pre-positioned. It also involved the selection of a structured linker (alpha helix) to maintain proper conformation. | ||
Line 151: | Line 152: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/2/24/HbiNlEV.jpg" class="img-responsive" space500 width="400" height="400"> |
</div> | </div> | ||
</div> | </div> | ||
</div> | </div> | ||
− | |||
<div class="space30"></div> | <div class="space30"></div> | ||
− | |||
− | |||
</section> | </section> | ||
<div class="clearfix"></div> | <div class="clearfix"></div> | ||
− | |||
<!-- start section 2 --> | <!-- start section 2 --> | ||
Line 170: | Line 167: | ||
<div class="container"> | <div class="container"> | ||
<div class="row"> | <div class="row"> | ||
+ | <h2 class="title wow bounce in up"><span style ="color:#000000"><span style="font-family:Armalite Rifle"><div align=center>Method</span></h2></span></div> | ||
− | |||
− | |||
− | |||
− | |||
<p><div align="justify"><span style ="color:#000000"><span style="font-family:courier new">To calculate and view our linkers, we used several bioinformatic tools and structural biology methods. | <p><div align="justify"><span style ="color:#000000"><span style="font-family:courier new">To calculate and view our linkers, we used several bioinformatic tools and structural biology methods. | ||
We offer a brief summary of these: | We offer a brief summary of these: | ||
Line 194: | Line 188: | ||
A trun-helix contains 3.6 residues and measures 5.4 Angstrom (1.5 Angstrom per residue).</li> | A trun-helix contains 3.6 residues and measures 5.4 Angstrom (1.5 Angstrom per residue).</li> | ||
</ul> | </ul> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
</p></span></div> | </p></span></div> | ||
Line 225: | Line 213: | ||
<u><b>Laccase <i>Thermus thermophilus</i> + Cytochrome C <i>Paracoccus denitrificans</i></b></u></span> | <u><b>Laccase <i>Thermus thermophilus</i> + Cytochrome C <i>Paracoccus denitrificans</i></b></u></span> | ||
<p><span style="font-family:courier new">The minimum distance between heme and the electron exchange surface of the laccase is: 29.84 Angstroms. </p></span> | <p><span style="font-family:courier new">The minimum distance between heme and the electron exchange surface of the laccase is: 29.84 Angstroms. </p></span> | ||
− | + | <div space="space 30"></div> | |
<p class="space 30"><span style="font-family:courier new">It exceeds the limit distance of 15 Angstroms. This construction seems not very optimized.</p></span> | <p class="space 30"><span style="font-family:courier new">It exceeds the limit distance of 15 Angstroms. This construction seems not very optimized.</p></span> | ||
Line 239: | Line 227: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/0/0f/1-TT-Para.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 270: | Line 258: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/9/9b/2-ColiPara.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 306: | Line 294: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/e/e9/3-Bs-Para.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 340: | Line 328: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/a/a6/4-BsShewa.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 374: | Line 362: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/1/1c/5-Coli-Shewa.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 407: | Line 395: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/0/08/6-ttShewa.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 439: | Line 427: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/d/d4/7-BsSyne.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 477: | Line 465: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/d/da/8-Coli_syne.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 514: | Line 502: | ||
<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
− | <img src=" | + | <img src="https://static.igem.org/mediawiki/2015/1/1b/9-TTsyne.jpg" class="img-responsive" space500 width="450" height="300"> |
</div> | </div> | ||
Line 532: | Line 520: | ||
</section> | </section> | ||
<div class="clearfix"></div> | <div class="clearfix"></div> | ||
− | |||
Line 544: | Line 531: | ||
<h1 class="blue">MORE INFORMATION ON FACEBOOK !</h1> | <h1 class="blue">MORE INFORMATION ON FACEBOOK !</h1> | ||
<ul class="list-inline space80 icon"> | <ul class="list-inline space80 icon"> | ||
− | <li><a href="https://www.facebook.com/iGEM.AMU?fref=ts"><img src=" | + | <li><a href="https://www.facebook.com/iGEM.AMU?fref=ts"><img src="https://static.igem.org/mediawiki/2015/e/ed/FacebookAMU.png" width="200" height="200" class="img-grey mautomargin"></a></li> |
</ul> | </ul> | ||
Line 552: | Line 539: | ||
</section> | </section> | ||
− | + | <div class="clearfix"></div> | |
<!-- start sponsors section --> | <!-- start sponsors section --> | ||
<section style="padding:50px 0px;" class="arrow_box-2"> | <section style="padding:50px 0px;" class="arrow_box-2"> | ||
Line 560: | Line 547: | ||
<div class="col-md-12 text-center"> | <div class="col-md-12 text-center"> | ||
<h2 class="gray">SPONSORS</h2> | <h2 class="gray">SPONSORS</h2> | ||
− | + | <ul class="list-inline space30 icon"> | |
− | + | <li><a href="https://www.corning.com/worldwide/en/products/life-sciences.html"> | |
− | + | <img src="https://static.igem.org/mediawiki/2015/8/87/Corninglogo.jpg" width="200" align="center" | |
− | + | class="img-grey mautomargin"></a></li> | |
− | + | <li><a href="http://www.crous-aix-marseille.fr/social/fsdie-social"> | |
− | + | <img src="https://static.igem.org/mediawiki/2015/1/18/KlP5G8h.jpg" | |
− | + | class="img-grey mautomargin" width="200" align="center"></a></li> | |
− | + | <li><a href="http://www.cnrs.fr/"> | |
− | + | <img src="https://static.igem.org/mediawiki/2015/8/8e/CNRSlogo.jpg" | |
− | + | width="200" class="img-grey mautomargin" align="center"></a></li> | |
− | <li><a href="http://www.mn-net.com/"><img src=" | + | <li><a href="https://www.qiagen.com/fr/"> |
− | <li><a href="https://fr.groupeonet.com/Onet-Proprete-et-Services"><img src=" | + | <img src="https://static.igem.org/mediawiki/2015/f/f1/Qialogo.jpg" width="200" align="center" |
− | <li><a href=" | + | class="img-grey mautomargin"></a></li> |
− | <li><a href="https://www.sigmaaldrich.com/france.html"><img src=" | + | <li><a href="http://www.univ-amu.fr/"> |
− | <li><a href="http://www.starlab.de/int/?l=5"><img src=" | + | <img src="https://static.igem.org/mediawiki/2015/3/38/EcfFf9Kw.png" |
− | <li><a href="http://fr.ambafrance-us.org/"><img src=" | + | class="img-grey mautomargin" width="200" align="center" ></a></li> |
− | <li><a href="https://www.neb.com/"><img src=" | + | <li><a href="http://polytech.univ-amu.fr/"> |
− | <li><a href="http://sciences.univ-amu.fr/"><img src=" | + | <img src="https://static.igem.org/mediawiki/2015/1/10/ILFZ36R.png" |
− | <li><a href="https://eu.idtdna.com/site"><img src=" | + | class="img-grey mautomargin" width="200" align="center"></a></li> |
− | + | <li><a href="http://www.grandluminy.com/"> | |
− | + | <img src="https://static.igem.org/mediawiki/2015/6/66/GandLlogo.jpg" width="200" align="center" | |
− | + | class="img-grey mautomargin"></a></li> | |
− | + | <li><a href="https://www.eppendorf.com/FR-fr/"> | |
+ | <img src="https://static.igem.org/mediawiki/2015/d/db/Eppendorflogo.jpg" width="200" align="center" | ||
+ | class="img-grey mautomargin"></a></li> | ||
+ | <li><a href="http://www.dutscher.com/frontoffice/home"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/1/10/Deutcherflogo.jpg" width="200" align="center" | ||
+ | class="img-grey mautomargin"></a></li> | ||
+ | <li><a href="http://www.mn-net.com/"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/1/1b/MNlogo.jpg" width="200" align="center" | ||
+ | class="img-grey mautomargin"></a></li> | ||
+ | <li><a href="https://fr.groupeonet.com/Onet-Proprete-et-Services"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/3/3d/5tokNzS.jpg" width="200" align="center" | ||
+ | class="img-grey mautomargin"></a></li> | ||
+ | <li><a href="http://www3.gehealthcare.fr/"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/b/bd/GEHlogo.jpg" width="200" | ||
+ | class="img-grey mautomargin" align="center" ></a></li> | ||
+ | <li><a href="https://www.sigmaaldrich.com/france.html"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/4/41/PUNXaNj.jpg" align="center" | ||
+ | class="img-grey mautomargin" width="200"></a></li> | ||
+ | <li><a href="http://www.starlab.de/int/?l=5"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/1/13/StarLablogo.jpg" align="center" | ||
+ | class="img-grey mautomargin" width="200" height="100"></a></li> | ||
+ | <li><a href="http://fr.ambafrance-us.org/"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/2/2b/M3ieC2R.jpg" align="center" | ||
+ | class="img-grey mautomargin" width="200" height="100"></a></li> | ||
+ | <li><a href="https://www.neb.com/"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/a/a9/Ll3uagr.jpg" align="center" | ||
+ | class="img-grey mautomargin" width="200"></a></li> | ||
+ | <li><a href="http://sciences.univ-amu.fr/"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/4/4a/FtFgEFj.jpg" align="center" | ||
+ | class="img-grey mautomargin" width="200"></a></li> | ||
+ | <li><a href="https://eu.idtdna.com/site"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/d/d9/IDTlogo.jpg" align="center" | ||
+ | class="img-grey mautomargin" width="200"></a></li> | ||
+ | </ul> | ||
Line 590: | Line 610: | ||
<div class="space20"></div> | <div class="space20"></div> | ||
</div> | </div> | ||
− | |||
</section> | </section> | ||
<!-- start footer --> | <!-- start footer --> |
Latest revision as of 00:07, 19 September 2015
Our idea
Method
To calculate and view our linkers, we used several bioinformatic tools and structural biology methods.
We offer a brief summary of these:
Swiss-PdbViewer :
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Gromacs :
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
VMD :
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
All these tools need a pdb file as input. The first step is to download the file pdb corresponding to each of the proteins on RCSB PDB (http://www.rcsb.org/pdb/home/home.do).
Then, you have to pre-position the two proteins using Swiss-pdb Viewer. The electron exchange surface must be up to 15 Angstrom from each other.
It is continued by a minimization step to eliminate steric strain. This calcul considers electrostatic forces, Van der Wall interactions etc…
A conformation is generated from these constraints. It is sufficient to take the coordinates of the N-term residue (A) and C-term (B) and to calculate the distance (AB) between the two to generate a linker suitable.
AB = √( (xA-xB)^2+ 〖(yA-yB)^2+(zA-zB)〗^2 )
A trun-helix contains 3.6 residues and measures 5.4 Angstrom (1.5 Angstrom per residue).
Our modelisation
Laccase Thermus thermophilus + Cytochrome C Paracoccus denitrificansThe minimum distance between heme and the electron exchange surface of the laccase is: 29.84 Angstroms.
It exceeds the limit distance of 15 Angstroms. This construction seems not very optimized.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance calculated between the C-term and N-term: 23.44 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKEAAAKEAAAKGG
The minimum distance between heme and the electron exchange surface of the laccase is: 15.2 Angstroms.
This construct is useful. It can be expected that the structural dynamics allow rappochement less than 15 Angstroms, making a possible oxidation of the cytochrome.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance calculated between the C-term and N-term is: 35.37 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKEAAAKEAAAKEAAAKGG
The minimum distance between heme and the electron exchange surface of the laccase is: 13 Angstroms.
It is one of our best constructions. The distance seems ideal for electron transfer. We just have to hope that its expression goes well on the bench.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance between the C-term and N-term is: 16.5 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKG
The minimum distance between heme and the electron exchange surface of the laccase is: 17 Angstroms.
We can hope to gain a few angstroms thanks to the dynamics of the structure.
Order of the construction: CtermLacc – LINKER – NtermCyt
Distance between the C-term and N-term is: 44.5 Angstroms
Linker sequence deducted : GGAEAAAKEAAAKAEAAAKEAAAKAEAAAKEAAAKGG
The minimum distance between heme and the electron exchange surface of the laccase is: 19.5 Angstroms.
We can hope to gain a few angstroms thanks to the dynamics of the structure.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance between the C-term and N-term is:55.48 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKEAAAKEAAAKEAAAKEAAAKEAAAKG
The minimum distance between heme and the electron exchange surface of the laccase is: 19.4 Angstroms.
Same analyse, we can hope to gain a few angstroms thanks to the dynamics of the structure.
Order of the construction: CtermLacc – LINKER – NtermCyt
Distance between the C-term and N-term is: 38.65 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKEAAAKEAAAKEAAAKG
The minimum distance between heme and the electron exchange surface of the laccase is: 15.29 Angstroms.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance between the C-term and N-term is:21.6 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKG
The minimum distance between heme and the electron exchange surface of the laccase is: 38.53 Angstroms.
It is the worst construction. The heme/copper laccase is way too far to allow oxidation.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance calculated between the C-term and N-term is: 40.44 Angstroms.
Linker sequence deducted : GGAEAAAKEAAAKEAAAKEAAAKEAAAKEAAAKGG
The minimum distance between heme and the electron exchange surface of the laccase is: 33.23 Angstroms.
It is one of the worst construction. The heme/copper laccase is way too far to allow oxidation.
Order of the construction: CtermCyt – LINKER – NtermLacc
Distance calculated between the C-term and N-term is: 40.6 Angstroms.
Linker sequence deducted : GAEAAAKEAAAKEAAAKEAAAKEAAAKG