AMBER Archive (2008)

Subject: Re: AMBER: study of protein stability in different ion using AMBER

From: David A. Case (case_at_scripps.edu)
Date: Sat Mar 15 2008 - 00:48:13 CDT

On Thu, Mar 13, 2008, Prem Prakash Pathak wrote:
>
> My protein is stable in NaCl. However it its stability decreases with
> the increasing concentration of the Ca2+ ions. I wanted to study this
> behavior of protein using Amber.
>
> I wanted to know how can i do the study in AMBER, about the stability
> of my protein in different solvent environment , at different
> concentration and pH condition.

It is unlikely that amber (or any MD simulation program) can attack this
problem in any quantitative way, although you *might* see some hints by
running simulations. You need to think about whether there are specific Ca+2
binding sites that you might try to identify. Looking at the work of David
Draper and co-workers (on Mg2+ effects) would be a good way to see some of the
complexities that arise in understanding divalent ion effects on biomolecules.

You might still want to study this problem, but be aware of the difficulties:
you can't just calculate the (thermal?) stability under different salt
conditions and compare to experiment.

...dac

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