[gmx-users] MD continuation

[Ruben M Buey]

Thanks a lot for your mail,
Just a little question more:
Suppose I want to see the changes in the switch I and switch II of a 
GTPase protein in response to GDP/GTP bound nucleotide. When I simulate 
the GTP state, an helix H moves away and when I simulate the GDP state 
the helix H does not move. Can I take the "final structure" of the GTP 
simulation, remove the gamma phosphate (i.e. GDP) and do another MD run 
to see if the helix H comes back to the original-GDP position?
I mean, if the changes produced by gamma phosphate are "reversibles" in 
the MD simulations, is this a control of the "reliability" of the 
simulation?
Does this makes sense?
Thanks a lot again,
Bests
Ruben

Xavier Periole escribió:

> Ruben M Buey wrote:
>
>> Does it make sense to simulate the GDP-bound state of a protein 
>> starting from the equilibrated structure of a MD simulaton of the 
>> GTP-bound state.
>> I mean, I have the structure of the GTP form but I do not have the 
>> GDP-bound structure. 
>
>
> It makes sense of course but the result is unknown. If you do not have 
> any control on the
> final structure of the GDP simulation (or mutant simulation) you will 
> face the problem of
> what is relevant in the changes (if any) happening during the GDP 
> simulation.
>
> One thing you can do is collect as much as possible information 
> conserning the GDP form
> of your protein and compare your simulation to this data.
>
> Marco Ceruso and myself did some nice work on GDP/GTP conformations 
> changes in
> transducin. Check the paper :
> "Molecular dynamics simulations of transducin: interdomain and front 
> to back
> communication in activation and nucleotide exchange."
> J Mol Biol. 2004 Apr 30;338(3):469-81.
>
> Hope it'll help.
> XAvier
>

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Ruben M Buey. PhD student. Lab 308
Centro de Investigaciones Biologicas
Consejo Superior de Investigaciones Cientificas
Dpt. Protein Function and Structure
C/ Ramiro de Maeztu, 9 
28040  Madrid   (SPAIN)
Phone:   34-918373112 ext 4380
Fax:     34-915360432
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