AMBER Archive (2007)

Subject: Re: AMBER: NMR vs. X-ray structures

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 12 2007 - 05:57:12 CDT

this is only one system, bust we do discuss some of the possible
issues. Ron Levy's lab also has a paper coming out in Proteins (may
be out now) comparing lots of nmr and xray structures.

Wickstrom, L., Bi, Y., Hornak, V., Raleigh, D. and Simmerling, C.,
"Reconciling the Solution and X-ray Structures of the Villin Headpiece
Helical Subdomain: Molecular Dynamics Simulations and Double Mutant Cycles
Reveal a Stabilizing Cation-Pi Interaction", Biochemistry, 46:3624-3634
(2007)

On 6/12/07, Sally Pias <sallypias_at_gmail.com> wrote:
>
> I am wondering whether anyone knows of a systematic study of the
> behavior of NMR versus X-ray protein structures during MD simulations.
> I noticed in the amber reflector archives that NMR structures are
> known to have a tendency to show less stability than X-ray structures
> (per Yong Duan, October 2003). I am looking for any publications that
> may demonstrate this trend and that may offer some explanation for it.
> Otherwise, I would be grateful for any explanation that you all might
> offer.
>
> I have naively carried out a series of MD simulations starting with an
> NMR protein structure (wild-type and in silico point mutants), using a
> 20 ps equilibration to 300 K. During subsequent 5 ns production runs,
> I am seeing RMSD's averaging 4 to 6 Angstroms. I later carried out
> identical simulations on a homologous protein, for which both NMR and
> X-ray structures exist. While the NMR structure again gave an RMSD
> peaking at 6 Angstroms over 5 ns, the X-ray structure's RMSD reached
> only 1.5 Angstroms over the same timescale.
>
> Do you think that a longer, more elaborate equilibration would lessen
> this discrepancy? Can I trust any of the NMR-based data I have
> gathered so far, or is the RMSD out of a believable range?
>
> Thank you for your help.
>
> Sally
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