The two state of the protein being well characterized by the 2 simulations, we focus now on finding any difference between the two.

Movement of the alpha helix

As you can see in our simulations, we weren't able to see a clear movement of the helix. It would have been the nicest result possible, because it would have validated the hypothesis of the helix being a rigid lever. Anyway, as our simulations reproduce nicely the B-factor of the crystallography from the RMSF, we can deduce that they are valide. The lack of movement probably results from a bad crystallography or more likely from a poor charge description of the FMN. We would need to do some quantum mechanic simulation to validate these, but we don't have the time in the perspective of the jamboree.

Sidechains involved in signal transmission from FMN to alpha helix

We learned from an article that the GLN513 seems to be involved in an hydrogen bond with FMN. We tried to monitore this bond in our dark light simulation without seeing anything.

same conclusion as before

Pbm with cristallo -> however we are consistent with the cristallo, because nothing moves in our results, but even in the initial cristallo, nothing moved :)

the active site of the Cys450, or above all on the space around the active site.