[gmx-users] Urea induced denaturation

[Douglas Grahame]

Thanks Justin, pervious experiments were not with Urea but I'll try
extending the simulation time further to 10 - 20ns and hopefully that will
do it re: seeing denaturation. Thanks again,

-Douglas Grahame
BSc. MSc. PhD. Candidate
dgrahame at uoguelph.ca

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
Justin Lemkul
Sent: July 23, 2014 6:50 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Urea induced denaturation



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

--
==================================================

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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