[gmx-users] Urea induced denaturation

[Justin Lemkul]

On 7/23/14, 6:46 PM, Douglas Grahame wrote:
> Hi everyone, just wondering if anyone can suggest some papers or links to
> sources for urea induced denaturation. I'm trying to look at protein
> stability of various mutants but simulated annealing and simulations at
> constant temperature up to 500 ps  haven't shown or reflected or wet lab
> data. Hoping to examine urea denaturation to assess the strength of a
> beta-barrel hydrophobic core. Any suggestions or hints in the right
> direction would be great! Thanks everyone,
>

500 ps is not nearly enough time to see anything relevant happening, independent 
of whatever conditions you're using.  The effects of simple thermal denaturation 
should be evident even within 10-20 ns, but everything you see is also a 
function of the force field and the quality of the urea parameters.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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