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Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

ABSTRACT: For a representative set of 64 nonhomologous proteins, each containing a structure solved by NMR and X-ray crystallography, we analyzed the variations in atomic coordinates between NMR models, the temperature (B) factors measured by X-ray crystallography, and the fluctuation dynamics predicted by the Gaussian network model (GNM). The NMR and X-ray data exhibited a correlation of 0.49. The GNM results, on the other hand, yielded a correlation of 0.59 with X-ray data and a distinctively better correlation (0.75) with NMR data. The higher correlation between GNM and NMR data, compared to that between GNM and X-ray B factors, is shown to arise from the differences in the spectrum of modes accessible in solution and in the crystal environment. Mainly, large-amplitude motions sampled in solution are restricted, if not inaccessible, in the crystalline environment of X-rays. Combined GNM and NMR analysis emerges as a useful tool for assessing protein dynamics.

SUBMITTER: Yang LW

PROVIDER: S-EPMC2760440 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature

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Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

Yang Lee-Wei LW Eyal Eran E Chennubhotla Chakra C Jee JunGoo J Gronenborn Angela M AM Bahar Ivet I

Structure (London, England : 1993) 20070601 6

For a representative set of 64 nonhomologous proteins, each containing a structure solved by NMR and X-ray crystallography, we analyzed the variations in atomic coordinates between NMR models, the temperature (B) factors measured by X-ray crystallography, and the fluctuation dynamics predicted by the Gaussian network model (GNM). The NMR and X-ray data exhibited a correlation of 0.49. The GNM results, on the other hand, yielded a correlation of 0.59 with X-ray data and a distinctively better cor ...[more]

PMID: 17562320

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Dataset Information

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

Publications

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

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