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

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 motions are curtailed by intermolecular contacts in the crystal environment causing a discrepancy between theory and experiments. Interestingly, the information conveyed by X-ray crystallography becomes more consistent with NMR models and computational predictions when ensembles of X-ray models are considered. Less precise (broadly distributed) ensembles indeed appear to describe the accessible conformational space under native state conditions better than B-factors. Our results highlight the importance of using multiple conformations obtained by alternative experimental methods, and analyzing results from both coarse-grained models and atomic simulations, for accurate assessment of motions accessible to proteins under native state conditions.