A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations.

ABSTRACT: A detailed analysis of high-resolution structural data and computationally predicted dynamics was carried out for a designed sugar-binding protein. The mean-square deviations in the positions of residues derived from nuclear magnetic resonance (NMR) models and those inferred from X-ray crystallographic B-factors for two different crystal forms were compared with the predictions based on the Gaussian Network Model (GNM) and the results from molecular dynamics (MD) simulations. GNM systematically yielded a higher correlation than MD, with experimental data, suggesting that the lack of atomistic details in the coarse-grained GNM is more than compensated for by the mathematically exact evaluation of fluctuations using the native contacts topology. Evidence is provided that particular loop moti

SUBMITTER: Liu L 

PROVIDER: S-EPMC2767477 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature