TY - JOUR
T1 - Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions
AU - Yang, Lee Wei
AU - Eyal, Eran
AU - Chennubhotla, Chakra
AU - Jee, Jun Goo
AU - Gronenborn, Angela M.
AU - Bahar, Ivet
PY - 2007/6/13
Y1 - 2007/6/13
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=34249945151&partnerID=8YFLogxK
U2 - 10.1016/j.str.2007.04.014
DO - 10.1016/j.str.2007.04.014
M3 - Article
C2 - 17562320
AN - SCOPUS:34249945151
SN - 0969-2126
VL - 15
SP - 741
EP - 749
JO - Structure
JF - Structure
IS - 6
ER -