[gmx-users] Protein in GdmCl solution
jalemkul at vt.edu
Tue Feb 19 02:58:47 CET 2013
On 2/18/13 9:54 AM, Biswajit Gorai wrote:
> Dear Justin,
> Thanks a lot for your reply.
> As u mentioned, I edited the mass as follows:
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB ch
> 1 CA 1 GDM C1 1 0.99610 12.010000
> 2 N2 1 GDM N1 2 -0.94930 14.010000
> 3 H 1 GDM H1 3 0.47530 1.008000
> 4 H 1 GDM H2 4 0.47530 1.008000
> 5 N2 1 GDM N2 5 -0.94930 14.010000
> 6 H 1 GDM H3 6 0.47530 1.008000
> 7 H 1 GDM H4 7 0.47530 1.008000
> 8 N2 1 GDM N3 8 -0.94930 14.010000
> 9 H 1 GDM H5 9 0.47530 1.008000
> 10 H 1 GDM H6 10 0.47530 1.008000
> I am dealing with a small basic protein of 60 aa.
> It is a very stable protein which maintains its structure even at 8 M Urea
> but 5M GdmCl can denature it (experimentally).
> In-silico (simulation) studies have done in hundreds of ns to denature
> their target proteins using chemical denaturants.
> Unfortunately, I don't have such computational power.
> I already denatured my protein at 423 K around ~40 ns.
> So combination of both (chemical and physical denaturants) should able to
> produce the expected result
> atleast below 40 ns or so (within available resources).
> But that is not happening, most surprisingly, even the temperature effect
> Showing GdmCl producing counteraction to temperature, which experimentally
> doesn't valid for my target.
The only advice I would provide is to follow an established protocol rather than
mess around haphazardly with things you hope will work. The other plain fact is
that if other simulations require hundreds of ns to manifest the desired
behavior, you should likely expect the same. You should stick to a given set of
experimental conditions and try to model it rather than trying to deconvolute
complex contributions to denaturation after the fact.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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