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Molecular and stochastic dynamics of proteins

Nadler, Walter and Brünger, Axel T. and Schulten, Klaus and Karplus, Martin (1987) Molecular and stochastic dynamics of proteins. Proceedings of the National Academy of Sciences of the United States of America, 84 (22). pp. 7933-7937. ISSN 0027-8424. PMCID PMC299450. doi:10.1073/pnas.84.22.7933.

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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.

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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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Subject Keywords:Brownian motion; computer simulations; correlation functions; intramolecular fluctuations; myoglobin; Mossbauer spectroscopy studies
Issue or Number:22
PubMed Central ID:PMC299450
Record Number:CaltechAUTHORS:NADpnas87
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:10007
Deposited By: Tony Diaz
Deposited On:05 Apr 2008
Last Modified:08 Nov 2021 21:04

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