MOLECULAR-DYNAMICS OF STAPHYLOCOCCAL NUCLEASE - COMPARISON OF SIMULATION WITH N-15 AND C-13 NMR RELAXATION DATA

Motional parameters for the atomic-level dynamics of staphylococcal nu clease are calculated from an Is-ns molecular dynamics simulation of t he liganded enzyme and from a 3.75-ns simulation of the unliganded enz yme and compared with motional parameters calculated from C-13 and N-1 5 NMR relaxation data. Order parameters for backbone N-H and C-alpha-H bond vectors are on average in good agreement with experiment, indica ting a similar degree of backbone flexibility. Somewhat greater flexib ility is seen in the simulation of unliganded SNase, consistent with s ome experimental data. Alanine C-alpha-C-beta and C-alpha-H order para meters agree to within 5% for simulation while NMR finds the former to be 30% smaller than the latter; thus experimental reexamination of (C H3)-C-13 relaxation may be worthwhile. Average simulated and experimen tal rotation rates for the more rapidly rotating alanine and leucine m ethyl groups are in agreement. However, simulation predicts a much lar ger range of methyl rotation rates than is observed experimentally. An alysis 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.