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Published November 15, 1987 | Published
Journal Article Open

Molecular and stochastic dynamics of proteins


The rapid fluctuations of protein atoms derived from molecular dynamics simulations can be extrapolated to longer-time motions by effective single-particle stochastic models. This is demonstrated by an analysis of velocity autocorrelation functions for the atoms of lysine side chains in the active site of RNase A. The atomic motions are described by a bounded stochastic model with the friction and noise parameters determined from a molecular dynamics simulation. The low-frequency relaxation behavior is shown to result from collisional damping rather than dephasing. Extrapolation of these results to the quasistochastic motion of the heme group in myoglobin provides an explanation of 57Fe Mossbauer spectroscopic data.

Additional Information

© 1987 by the National Academy of Sciences. Contributed by Martin Karplus, May 29, 1987. The authors thank C. L. Brooks, III, P. Tavan, and H. Treutlein for helpful discussions and assistance with some of the computations. This work was supported in part by the National Institutes of Health. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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