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Proteins. 2015 May;83(5):922-30. doi: 10.1002/prot.24789. Epub 2015 Mar 25.

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

Author information

1
Graduate Group in Biochemistry and Molecular Biophysics and the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104.

Abstract

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(2) NH ) 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(2) NH  < 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(2) axis . A calibration curve for backbone entropy vs. O(2) NH 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(2) NH 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(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements.

KEYWORDS:

NMR relaxation; backbone motion; conformational entropy; molecular dynamics; protein motion

PMID:
25739366
PMCID:
PMC4400257
DOI:
10.1002/prot.24789
[Indexed for MEDLINE]
Free PMC Article

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