Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions

Lee Wei Yang, Eran Eyal, Chakra Chennubhotla, Jun Goo Jee, Angela M. Gronenborn, Ivet Bahar

Research output: Contribution to journalArticlepeer-review

114 Scopus citations

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.

Original languageEnglish
Pages (from-to)741-749
Number of pages9
JournalStructure
Volume15
Issue number6
DOIs
StatePublished - 13 Jun 2007

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