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The effects of rigid motions on elastic network model force constants
Author(s) -
Lezon Timothy R.
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24014
Subject(s) - force constant , anisotropy , rigid body , constant (computer programming) , physics , dynamics (music) , statistical physics , experimental data , classical mechanics , mathematics , molecule , computer science , optics , quantum mechanics , statistics , acoustics , programming language
Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model's single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here, we investigate the differences between calculated values of force constants and data from NMR and X‐ray structures. We find that X‐ray B factors carry the signature of rigid‐body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over‐fitting. No correlation is found between force constants fit to NMR data and those fit to X‐ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. Proteins 2012; © 2011 Wiley Periodicals, Inc.