期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 83, 期 5, 页码 922-930出版社
WILEY
DOI: 10.1002/prot.24789
关键词
protein motion; backbone motion; conformational entropy; molecular dynamics; NMR relaxation
资金
- NIH [GM102447, T32 GM008275]
- NRBSC [RC2GM093307]
Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O-NH(2)) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O-NH(2)<0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O-axis(2). A calibration curve for backbone entropy vs. O-NH(2) is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O-NH(2) changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O-axis(2) values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. Proteins 2015; 83:922-930. (c) 2015 Wiley Periodicals, Inc.
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