[gmx-users] How to find the mutation effect?

[Justin Lemkul]

On Sun, Dec 15, 2013 at 1:42 PM, xiao <helitrope at 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

-- 

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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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