Re: [AMBER] How to study protein-protein complex are stabilized/destabilized upon complexation?

From: Carlos Simmerling <>
Date: Tue, 14 Dec 2010 12:29:15 -0500

what do you mean by "stabilized"? do you mean thermodynamic stability of the
protein fold? there is currently no way of directly calculating that,
thought you might estimate it in some ways (Amber does not do this). Or do
you mean "stabilized" as in less fluctuation? if that's what you want, you
can make that claim using RMSF.

On Tue, Dec 14, 2010 at 12:26 PM, Catein Catherine

> Dear Sir/Madam,
> I am trying to study a protein-protein complex using amber. I want to
> examine if the binding between protein-protein could stabilize or destabilze
> the whole complex.
> I have calculate the MM-GBSA binding energy, I have also calculate the
> b-factor rmsf of the protein individually and in their complex form.
> I got the binding energy is ~ negative 100 kcal/mol. I also found the
> rmsf, I found the individual rmsf was reduced from 600 to 300.
> Can I define the protein-protein complex stabilized? Should I use any
> other additional approaches to proof that protein-protein complexes are
> indeed stabilized upon complexation?
> Best regards,
> Cat
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Received on Tue Dec 14 2010 - 10:00:02 PST
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