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Team:EPF-Lausanne/Results/ELS
From 2009.igem.org
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We ploted the angle between the helix and and a strand of the beta sheet. As in the light state we don't see a clear movement. | We ploted the angle between the helix and and a strand of the beta sheet. As in the light state we don't see a clear movement. | ||
[[Image:2v0w_sim_angoli.jpg|center]] | [[Image:2v0w_sim_angoli.jpg|center]] | ||
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| + | We also redid the same experiments as in the dark state. | ||
| + | Here is the plot of the dihedral angle of GLN513 and ASN414. | ||
| + | [[Image:2v0w_dihed_513_414.jpg|center]] | ||
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Revision as of 19:16, 19 October 2009
We run a a 62ns simulation on the 2v0w light state using 32 processors. Here is a video.
Validation of the simulation
Here are the values of pressure, temperature and volume for this run.
The rmsd along the run gives:
And the rmsf is:
Analysis of the simulation
As for the dark state, we tried to find a change in the j-alpha helix then looked at the comportment of the residues.
We ploted the angle between the helix and and a strand of the beta sheet. As in the light state we don't see a clear movement.
We also redid the same experiments as in the dark state. Here is the plot of the dihedral angle of GLN513 and ASN414.
An interesting residue to study in the light state is the residue n° 450, which is the cystein that reacts with the cofactor. Here we plot the dihedral angle of this residue to see how many time the cystein point toward the FMN:
