Re: AMBER: denaturing salt conditions

From: Jiri Sponer <>
Date: Sun, 4 Mar 2007 01:28:28 +0100 (MET)

I am not sure what exactly is your aim.
However, you need to take into consideration the
timescale of MD. You may expose your in silico system to
"denaturating" conditions, but there is no denaturation or unfolding during MD
simply because denaturation or unfolding needs longer than few ns.
Sometimes it is an invaluable advantage, sometimes frustrating disadvantage.
Depending on what is your exact aim.
Simulations mimic a hypothetical ns-scale
truly single molecule experiment with a given start within
the approximation of the quite simple force field. Nothing more,
nothing less.

Best wishes, jiri

Jiri Sponer, D.Sc.
Institute of BiopHysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133
Senior Wellcome Trust International Research Fellow for Biomedical Science

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> Hello Amberites,
> I have a quick question regarding oligeric interactions in proteins. I know that if we model a protein in 8M urea, that the protein should unfold. But if I have a dimer, there should be something less harsh that will let the two monomers separate. I thought I might have known this from undergrad some years ago, but don't have a quick fix handy. Perhaps a mild combination of salt and/or pH? If any of you have some ideas, I'd be all ears.
> Main reason for asking is, I have an xtal structure that is a dimer, but I want to run some kinetic analyses on the monomer, and rather than just stripping the dimer in half, I thought that I could set up the assay conditions to represent those that would support a the monomer. Not eloquently worded, but if anyone has any ideas, please advise.
> Sean
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Received on Sun Mar 04 2007 - 06:08:13 PST
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