On Sun, Dec 15, 2013 at 1:42 PM, xiao <helitr...@126.com> wrote:

> Dear all,
>
> I am doing a MD on a mutant protein which is unstable from exprient.
> However, i found no difference between the wild type and the mutant protein
> from md, the structure and the rmsd are very similar in the mutant and the
> wild type.
>
> Can anyone tell me how to tackle this problem?
>
>
It depends on a large number of factors.  When you say the protein is
unstable, does it ever actually fold?  Does it fold into a metastable
state?  How has stability been determined experimentally, and most
importantly, over what time frame?  If you're talking differences in
half-life of even seconds, you'll never see that via MD.  The exact
approach is also a function of the force field and its inherent caveats or
deficiencies and the sampling in your simulation.  Are you doing one
simulation and hoping to see a difference, or are you running multiple
simulations/conducting REMD?

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441


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