AMBER: NMR vs. X-ray structures

From: Sally Pias <>
Date: Mon, 11 Jun 2007 23:22:19 -0600

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

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.

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Received on Wed Jun 13 2007 - 06:07:28 PDT
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