Hi,
Don't you have any apo and holo X-ray structure of the protein, to check that
you tend to model the correct ligand free structure at the end of the
dissociation process ?
If not, you can just check the 'convergence' of the final structure with a
longer simulation and see if they go towards the same structure.
In fact, you should in any case have a longer simulation, just to check the
convergence of the PMF curve with simulation time.
Hopes this helps.
Good luck.
jerome
Selon Catein Catherine <askamber23.hotmail.com>:
>
> Dear Sir/Madam,
>
> I have done a PMF for a protein-drug dissociation process.
>
> Large conformation change in the protein was observed. It opens up the space
> for the drug to dissociate from the binding site. I tends to interprete that
> as a conformation change during drug dissociation process.
>
> However, could the large conformational change be only artifacts of fast
> pulling, because the timescales required for a partial protein unfolding is
> not consistent with experimental dissociation rates?
>
> Could you mind to comments on how to interprete the conformation change in
> PMF of drug-dissociation?
>
> Best regards & thanks,
>
> Catherine
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--
Jérôme Golebiowski, Ph D. HDR, Asst. Pr.
LCMBA
UMR 6001 CNRS - University of Nice Sophia Antipolis
Molecular Modeling Team
06108 Nice cedex 2, France
tel: +33 (0)4 92 07 61 03
http://www.unice.fr/lcmba
http://www.unice.fr/lcmba/golebiowski
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Received on Thu Apr 07 2011 - 10:00:04 PDT
