Team:EPF-Lausanne/Results

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=Fusion of the LOV domain and the trpR DNA-binding domain=
=Fusion of the LOV domain and the trpR DNA-binding domain=
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The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD. We were then able to visualize the different proteins tried by Sosnick.
The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD. We were then able to visualize the different proteins tried by Sosnick.
The working protein, that we call LovTAP is the result of the fusion at PHE22 of trpR and can be seen on the next video. The general LOV domain is in yellow. Please note the chromophore called Flavin (FMN) in red in the center of LOV2. The trpR dna binding domain is in orange and DNA in gray.
The working protein, that we call LovTAP is the result of the fusion at PHE22 of trpR and can be seen on the next video. The general LOV domain is in yellow. Please note the chromophore called Flavin (FMN) in red in the center of LOV2. The trpR dna binding domain is in orange and DNA in gray.
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* @ALA12: same remarks as for the previous. Furthermore, it is clear that LOV is in interaction with bound DNA.
* @ALA12: same remarks as for the previous. Furthermore, it is clear that LOV is in interaction with bound DNA.
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<br><center><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/FQ-xXnKAYEE&hl=fr&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/FQ-xXnKAYEE&hl=fr&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></center></br>
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=Equilibration of dark state=
=Equilibration of dark state=
We run an equilibration of 80ns on the dark state (2v0u).
We run an equilibration of 80ns on the dark state (2v0u).

Revision as of 13:22, 18 October 2009






Results of Modeling



Fusion of the LOV domain and the trpR DNA-binding domain

The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD. We were then able to visualize the different proteins tried by Sosnick. The working protein, that we call LovTAP is the result of the fusion at PHE22 of trpR and can be seen on the next video. The general LOV domain is in yellow. Please note the chromophore called Flavin (FMN) in red in the center of LOV2. The trpR dna binding domain is in orange and DNA in gray.

The fusion was made in VMD by aligning the alpha helix of both domains on the backbone of 3 residues. The secondary structure is quite strong and conserved, what makes this fusion realistic.

         Click here to see an example of code used in VMD for the fusion


We also modelized the other fusion tried by Sosnick.

  • @MET11
  • @ALA12
  • @GLU13
  • ...
  • @PHE22
  • ...
  • @LEU25

         Clear here to view the other fusions

Equilibration of dark state

We run an equilibration of 80ns on the dark state (2v0u).

Here is a movie over the trajectory file.

Validation of the simulation

Here we look at the output to check input parameters.

The raw data for the equilibration match what we set for the NPT. Pressure and temperature are kept constant using namd dynamic. The volume is quite constant as well.

2v0ueq.jpg

Then we computed the evolution of the rmsd compared to the first timestep of equilibration. We see that there is a plateau after ~40ns, which means that our system's energy is reaching a minimum. That's clearly what we expected.

2v0u rmsd.jpg

The comparison of the RMSF over the simulation to the beta factor measured during crystallography is a nice validation of our simulation. We get quite similar curves, with some differences at one end of the protein. We see in the movie that this part moves a lot.

2v0u rmsf.jpg

Analysis of the simulation

We have organized our analysis on 2 main ideas:

  • Find a structural change in the j-alpha helix based on the simulation using namd.
  • Find residues showing different comportment in dark and light state

First, we start by looking at the angle between the beta sheet and the j-alpha helix.

         Click here to see the code used in VMD to get angle data

We get a quite constant value. It will be more interesting to compare this graph to the light state.

2v0u angoli.jpg

The residues 513 seems to be involved in stabilisation of FMN through hydogen bonds. There is a picture of the situation, residue ASN 414 is on the left, GLN513 in the middle and the FMN is in red. All the hydrogen bonds we investigated over the simulation are pictured.

2v0u 414 513 FMN.jpg

Equilibration of light state

After having modified some parameters in the parameter files, here is the movie concerning the light state of the protein with the FMN: Light State

Light state

Analysis

  • Maxwell-Boltzmann Energy Distribution

We obtain the following histogramm! Energy


  • Temperature

Using EXCEL, we obtain the following graph, which represents the evolution of the temperature in function of time:
Temp(t).png
The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.


  • Density

Using EXCEL, we obtain the following graph, which represents the evolution of the density in function of time:
Density.jpg
The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.


  • Pressure

Here is a small plot of pressure and temperature in function of time Run


  • RMSD


We obtain the following picture:
RMSD CA per res.jpg

RMSD of residue within 3 angström of the FMN

Resid 3A.jpg

We can see that the residues that move the most are the residue number: 425, 451, 453



RMSD of residue within 6 angström of the FMN

Resid 6A.jpg
We can see that the residues that move the most are the residue number: 424, 425, 464, 468


  • RMSD of selected atoms compared to initial position along time

Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal.
Rmsd.jpg


Here is what we got with FIRST_FRAME=1115 REFERENCE_FRAME=1115. Average=921.477, standard deviation=202.1708
RMSD plateau.jpg


FIRST_FRAME=0 REFERENCE_FRAME=0. The difference of the sum probably comes from the new selection of atoms from the backbone. We should compute an average value to normalize amplitude. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393
RMSD COMPLETE RUN.jpg


  • Salt bridges

Here is a plot for one of the bridges. We have to look for the max distance for a salt bridge. Salt bridge.jpg


  • RMSF

2v02 1ns rmsf.jpg

This is a 1 nanosecond NPT run at 300°K. We hope to see a RMSF curve identical to the beta factor. It should only be shifted higher because of the increased temperature. But having a similar tendency would mean our simulation show oscillations similar to what was observed during crystallography. This is really a quite nice validation of our run!


Differential analysis

Some useful distances

  • Bond between Gln497 and Lys533 in dark state

bond1


  • Bond between Gln475 and Lys533 in dark state

bond2