Web Release Date: May 19,
Molecular Dynamics of Staphylococcal Nuclease: Comparison of Simulation with 15N and 13C NMR Relaxation Data
and
Contribution from the Chemistry Department, Florida International University, Miami, Florida 33199, and Laboratory of Structural Biology, Division of Computer Research and Technology, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
Received July 3, 1997
Revised Manuscript Received October 16, 1997
Abstract:
Motional parameters for the atomic-level dynamics of
staphylococcal nuclease are calculated from
an 18-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
13C and 15N NMR relaxation data.
Order
parameters for backbone N-H and C
-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-C
and C-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 13CH3
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.
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