Team:EPF-Lausanne/Modeling

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= Modeling =
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Theory" onMouseOver="document.MyImage4.src='https://static.igem.org/mediawiki/2009/thumb/8/83/Theory_nb.jpg/150px-Theory_nb.jpg';" onMouseOut="document.MyImage4.src='https://static.igem.org/mediawiki/2009/thumb/c/c9/Theory.jpg/150px-Theory.jpg';">
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==To do==
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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;- Model allosteric interactions between LOVTAP & TrpR:
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Implementation" onMouseOver="document.MyImage5.src=' https://static.igem.org/mediawiki/2009/thumb/3/3c/Impl_nb.png/150px-Impl_nb.png';" onMouseOut="document.MyImage5.src='https://static.igem.org/mediawiki/2009/thumb/6/65/Impl.png/150px-Impl.png';">
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:What will be done:
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<img src="https://static.igem.org/mediawiki/2009/thumb/6/65/Impl.png/150px-Impl.png" name="MyImage5"></a>
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:- Model of LOVTAP in dark phase
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:- Model of LOVTAP in light phase
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:- Characterize how the J-alpha helix changes
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:- Model sturctural 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.
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<span style="color:midnightblue">We will follow the following article protocol: </span>
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Analysis" onMouseOver="document.MyImage6.src='https://static.igem.org/mediawiki/2009/thumb/0/0c/Analysis_nb.jpg/150px-Analysis_nb.jpg';" onMouseOut="document.MyImage6.src='https://static.igem.org/mediawiki/2009/thumb/8/84/Analysis.jpg/150px-Analysis.jpg';">
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<br> Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, 91, 3630-3639, 2006 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed])
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<img src="https://static.igem.org/mediawiki/2009/thumb/8/84/Analysis.jpg/150px-Analysis.jpg" name="MyImage6"></a></center>
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<br>
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<br>
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<font size="6" color="#007CBC"><i>Modeling overview</i></font>
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<br>
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----
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<br>
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;- Model the fusion of LOV domain with other transcription factors
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==Protein domain of interest==
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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.
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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.
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For more information about LOVTAP protein please [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP click here].
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<br><br>
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==Goal==
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<br><br>
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==Starting material==
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Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]:
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:[http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0W Light activated LOV domain]
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==Implementation of the simulation==
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:[http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0U Dark LOV domain]
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Steps are explained in a little bit more detail on this page: [[Team:EPF-Lausanne/Modeling/Simulation|Simulation]]
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[[Team:EPF-Lausanne/Modeling/Movies|Movies]]
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These crystallographies were done by [http://www.ncbi.nlm.nih.gov/pubmed/18001137 Halavaty et al.].
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<br><br>
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==Molecular dynamics: a little theory==
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==To envisage ==
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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.
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<br>- Molecular mutationnal assay
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==Already done==
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<p>
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<br> We generated all the files needed to do the simulation, thanks to the tutorial of NAMD, which can be found on the following page:
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<a href="javascript:ReverseDisplay('hs1')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to expand</a>
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<br> http://www.ks.uiuc.edu/Training/Tutorials/
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</p>
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Here is our first movie from the modeling, showing the behavior of the protein in the dark state condition:
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<div id="hs1" style="display:none;">
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[[Media:2v0u_dark_state.mov | Dark State]]
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<p>
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After having modified some parameters in the parameter files, here is our second movie, concerning the light state of the protein this time, with the FMN:
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This potential energy can be divided into:
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[[Media:Light_FMN_without_water.mov‎  | Light State with FMN without water]]
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<h3>The non-bonded interactions:</h3>
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<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.
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<center>
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<img src="https://static.igem.org/mediawiki/2009/d/da/Lennard_jones_vdw_forces.jpg">
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<img src="https://static.igem.org/mediawiki/2009/thumb/f/f1/Lennard_jones.jpg/300px-Lennard_jones.jpg">
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<center><i><u>Lennard-Jones pair potential showing the r<sup>−12</sup> and r<sup>−6</sup> contributions</u></i></center>
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</center></li>
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<br>
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<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
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<center><img src="https://static.igem.org/mediawiki/2009/thumb/4/42/Coulomb.jpg/200px-Coulomb.jpg"></center>
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</li>
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<br><br><br>
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<h3>The bonded interactions:</h3>
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Angles, bonds and dihedral angles have to be taken into account:
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<br>
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<center><img src="https://static.igem.org/mediawiki/2009/thumb/2/28/Bonded.jpg/400px-Bonded.jpg"></center>
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<br><br>
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To understand a bit more, you can see the following article:
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<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>
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<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>
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<br><br>
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==Steps==
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===Minimization===
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===Equilibration===
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===Analysis and validation===
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===Simulation===
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===Atom movement analysis===
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<br><br>
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==References==
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<br><br>
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==Analysis methodology==
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<br><br>
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==Results==
 +
<br><br>
 +
 +
==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
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:- RMS between light state and dark state
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:- length between the two arms N C
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:- only cytochrome with interactions in light state and dark state
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<br><br>
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==To envisage ==
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<br>- Molecular mutational assay
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Latest revision as of 08:34, 21 September 2009



Contents

                               


Modeling overview


Protein domain of interest

Our protein of interest is LOVTAP. This protein was sythetically engineered by 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 RCSB:

Light activated LOV domain
Dark LOV domain

These crystallographies were done by 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.

         Click here to expand



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



Retrieved from "http://2009.igem.org/Team:EPF-Lausanne/Modeling"