NMR Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Timescales.
Biochemistry. 2011 Mar 9;
Authors: Salmon L, Bouvignies G, Markwick PR, Blackledge M
A complete description of biomolecular activity requires an understanding of the nature and the role of protein conformational dynamics. In recent years novel NMR-based techniques have emerged that provide hitherto inaccessible detail concerning biomolecular motions occurring on physiologically important timescales. Residual dipolar couplings (RDCs) provide precise information about time and ensemble averaged structural and dynamic processes with correlations times up to the millisecond, and thereby encode key information for understanding biological activity. In this review we present the application of two very different approaches to the quantitative description of protein motion using RDCs. The first is purely analytical, describing backbone dynamics in terms of diffusive motions of each peptide plane, using extensive statistical analysis to validate the proposed dynamic modes. The second is based on restraint-free accelerated molecular dynamics simulation, providing statistically sampled free-energy weighted ensembles that describe conformational fluctuations occurring on timescales from the pico to the millisecond, at atomic resolution. Remarkably the results from these two approaches converge closely in terms of distribution and absolute amplitude of motions, suggesting that this kind of combination of analytical and numerical models is now capable of providing a unified description of protein conformational dynamics in solution.
PMID: 21388216 [PubMed - as supplied by publisher]
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Mark V. Berjanskii and David S. Wishart
Journal of Biomolecular NMR; 2008; 40(1); pp 31-48
Abstract:
Protein flexibility lies at the heart of many protein–ligand binding events and enzymatic activities. However, the experimental measurement of protein motions is often difficult, tedious and error-prone. As a result, there is a considerable interest in developing simpler and faster ways of quantifying protein flexibility. Recently, we described a method, called Random Coil Index (RCI), which appears to be able to...
NMR Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Timescales.
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