Molecular dynamics of staphylococcal nuclease:: Comparison of simulation with 15N and 13C NMR relaxation data

Motional parameters for the atomic-level dynamics of staphylococcal nuclease are calculated from an Is-ns molecular dynamics simulation of the liganded enzyme and from a 3.75-ns simulation of the unliganded enzyme and compared with motional parameters calculated from C-13 and N-15 NMR relaxation data. Order parameters for backbone N-H and C-alpha-H bond vectors are on average in good agreement with experiment, indicating a similar degree of backbone flexibility. Somewhat greater flexibility is seen in the simulation of unliganded SNase, consistent with some experimental data. Alanine C-alpha-C-beta and C-alpha-H order parameters agree to within 5% for simulation while NMR finds the former to be 30% smaller than the latter; thus experimental reexamination of (CH3)-C-13 relaxation may be worthwhile. Average simulated and experimental rotation rates for the more rapidly rotating alanine and leucine methyl groups are in agreement. However, simulation predicts a much larger range of methyl rotation rates than is observed experimentally. Analysis of methyl rotations in a variety of environments indicates that the variation in the simulated methyl rotation rates is due to steric (van der Waals) interactions.