Re: AMBER: testing protein stability

From: Carlos Simmerling <>
Date: Fri, 22 Jun 2007 07:06:16 -0400

you're right that this is a very difficult problem. one can barely test
stability for peptides of 10-20 residues. Your heating protocol will compare
unfolding rates,
which may be related to stability but may not. you may want to check to see
if the
experiment has measured that. even if you do the unfolding, you will need
many runs to
get reliable statistics since the distribution of unfolding times for a
single sequence
may well be wider than the difference between average time for two
you might be better off doing free energy calculations where you mutate the
in the protein and again in a peptide model for the unfolded state, and use
that to
estimate the effect on stability.

On 6/22/07, Sally Pias <> wrote:
> I would like to use AMBER to test the stability of a protein following
> mutation. The three-dimensional structure of the wild-type protein is
> known, and I have introduced in silico mutations using DeepView (Swiss
> PDB Viewer). However, I am not sure if testing stability with MD
> simulations is a reasonable goal. If so, what kind of protocol would
> one use?
> I had planned to heat up the wild-type and mutant proteins in separate
> MD simulations, in order to identify a temperature threshold for the
> stability of each. By comparing the thresholds, I could get a measure
> of the relative stability of the mutant vs. the wild-type protein.
> I have already conducted a 5 ns production run for the mutant and
> found that it was stable on that timescale at 300 K, with explicit
> solvent. Still, the question is whether the mutant polypeptide would
> actually fold into the same three-dimensional structure as the
> wild-type and, if so, whether its dynamics and stability would be
> similar to those of the wild-type structure. I think the protein is
> probably too large (185 residues) for running a folding simulation.
> Thus, I am trying to test whether the mutant would be stable if it did
> take on the exact fold of the wild-type protein. (The mutations
> disrupt a zinc ion binding site that is likely to be involved in
> stabilizing the structure.)
> Any guidance would be appreciated.
> Thanks,
> Sally Pias
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Received on Sun Jun 24 2007 - 06:07:41 PDT
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