Paper Citing NAMD - Abstract
Sharp, Kim A.; O'Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua
On the relationship between NMR-derived amide order parameters and protein backbone entropy changes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:922-930, MAY 2015
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.
