Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.
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.
Yang
Lee-Wei
LW
Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA.
Eyal
Eran
E
Chennubhotla
Chakra
C
Jee
JunGoo
J
Gronenborn
Angela M
AM
Bahar
Ivet
I
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
D011506:Proteins