[gmx-users] Protein in GdmCl solution

[Justin Lemkul]

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
> argeB
>        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
> nullifies.
> 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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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