Team:EPF-Lausanne/Modeling
From 2009.igem.org
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==Protein domain of interest== | ==Protein domain of interest== | ||
- | [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP LOVTAP] | + | Our protein of interest is [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP LOVTAP]. This protein was sythetically engineered by [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18667691 Sosnick] group. It is a fusion protein between a LOV domain (Avena Sativa phototropin 1) and the E. Coli tryptophan repressor. |
- | + | This protein undergoes changes under light activation as shown by Sosnick et al, in fact when the protein is activated by light it binds DNA and inversely. | |
+ | For more information about LOVTAP protein please [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP click here]. | ||
+ | <br><br> | ||
==Goal== | ==Goal== | ||
- | + | <br><br> | |
==Starting material== | ==Starting material== | ||
+ | Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]: | ||
+ | :[http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0W Light activated LOV domain] | ||
+ | |||
+ | :[http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0U Dark LOV domain] | ||
+ | |||
+ | These crystallographies were done by [http://www.ncbi.nlm.nih.gov/pubmed/18001137 Halavaty et al.]. | ||
+ | <br><br> | ||
==Molecular dynamics: a little theory== | ==Molecular dynamics: a little theory== | ||
- | + | Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy. | |
- | == | + | <html> |
+ | <script type="text/javascript" language="JavaScript"><!-- | ||
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- | = | + | <p> |
+ | <a href="javascript:ReverseDisplay('hs1')"> Click here to expand</a> | ||
+ | </p> | ||
- | == | + | <div id="hs1" style="display:none;"> |
+ | <p> | ||
+ | This potential energy can be divided into: | ||
+ | |||
+ | <h3>The non-bonded interactions:</h3> | ||
+ | <li>The <i>Lennard-Jones potential</i> is the most commonly used form, with two parameters: σ, the diameter, and ε, the well depth. It takes into account the Van der Waals forces. It represents the non-bonded forces and the total potential energy can be calculated from the sum of energy contributions between pairs of atoms. | ||
+ | <center> | ||
+ | <img src="https://static.igem.org/mediawiki/2009/d/da/Lennard_jones_vdw_forces.jpg"> | ||
+ | | ||
+ | <img src="https://static.igem.org/mediawiki/2009/thumb/f/f1/Lennard_jones.jpg/300px-Lennard_jones.jpg"> | ||
+ | |||
+ | <center><i><u>Lennard-Jones pair potential showing the r<sup>−12</sup> and r<sup>−6</sup> contributions</u></i></center> | ||
+ | </center></li> | ||
+ | <br> | ||
+ | <li>when electrostatic charges are present, we add the <i>Coulomb force</i>, where Q1, Q2 are the charges and ϵ0 is the permittivity of free space | ||
+ | <center><img src="https://static.igem.org/mediawiki/2009/thumb/4/42/Coulomb.jpg/200px-Coulomb.jpg"></center> | ||
+ | </li> | ||
+ | <br><br><br> | ||
+ | <h3>The bonded interactions:</h3> | ||
+ | Angles, bonds and dihedral angles have to be taken into account: | ||
+ | <br> | ||
+ | <center><img src="https://static.igem.org/mediawiki/2009/thumb/2/28/Bonded.jpg/400px-Bonded.jpg"></center> | ||
+ | <br><br> | ||
+ | |||
+ | To understand a bit more, you can see the following article: | ||
+ | <a href="https://static.igem.org/mediawiki/2009/3/3e/Introduction_to_molecular_Dynamics_Simulation.pdf">Introduction to Molecular Dynamics Simulation - Michael P. Allen</a> | ||
+ | |||
+ | |||
+ | <p align="center" class="style1"><a href="#top"><img src="https://static.igem.org/mediawiki/2009/thumb/0/06/Up_arrow.png/50px-Up_arrow.png" alt="Back to top" border="0"></a><br></p> | ||
+ | <br> | ||
+ | |||
+ | </p> | ||
+ | </div> | ||
+ | </html> | ||
+ | <br><br> | ||
+ | ==Steps== | ||
+ | ===Minimization=== | ||
+ | ===Equilibration=== | ||
+ | ===Analysis and validation=== | ||
+ | ===Simulation=== | ||
+ | ===Atom movement analysis=== | ||
+ | <br><br> | ||
+ | ==References== | ||
+ | <br><br> | ||
+ | ==Analysis methodology== | ||
+ | <br><br> | ||
+ | ==Results== | ||
+ | <br><br> | ||
==To do== | ==To do== | ||
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:- only cytochrome with interactions in light state and dark state | :- only cytochrome with interactions in light state and dark state | ||
- | + | <br><br> | |
- | + | ||
==To envisage == | ==To envisage == | ||
<br>- Molecular mutational assay | <br>- Molecular mutational assay |
Latest revision as of 08:34, 21 September 2009
Contents |
Protein domain of interest
Our protein of interest is LOVTAP. This protein was sythetically engineered by [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18667691 Sosnick] group. It is a fusion protein between a LOV domain (Avena Sativa phototropin 1) and the E. Coli tryptophan repressor.
This protein undergoes changes under light activation as shown by Sosnick et al, in fact when the protein is activated by light it binds DNA and inversely.
For more information about LOVTAP protein please click here.
Goal
Starting material
Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]:
- [http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0W Light activated LOV domain]
- [http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0U Dark LOV domain]
These crystallographies were done by [http://www.ncbi.nlm.nih.gov/pubmed/18001137 Halavaty et al.].
Molecular dynamics: a little theory
Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy.
Steps
Minimization
Equilibration
Analysis and validation
Simulation
Atom movement analysis
References
Analysis methodology
Results
To do
- - Model allosteric interactions between LOVTAP & TrpR
- What will be done:
- - Model of LOVTAP in dark phase
- - Model of LOVTAP in light phase
- - Characterize how the J-alpha helix changes
- - Model structural changes that enhance the switch feature of LOVTAP e.g. in dark phase: really weak interaction between LOVTAP and the corresponding DNA sequence, in light phase: strong binding of LOVTAP on DNA.
- - Between Light state and Dark State
- - RMS between light state and dark state
- - length between the two arms N C
- - only cytochrome with interactions in light state and dark state
To envisage
- Molecular mutational assay