title: 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.
authors.affiliation: Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA.
authors.forename: Lee-Wei
authors.initials: LW
authors.lastname: Yang
authors.forename: Eran
authors.initials: E
authors.lastname: Eyal
authors.forename: Chakra
authors.initials: C
authors.lastname: Chennubhotla
authors.forename: JunGoo
authors.initials: J
authors.lastname: Jee
authors.forename: Angela M
authors.initials: AM
authors.lastname: Gronenborn
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008956:Models, Chemical; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins