Molecular and stochastic dynamics of proteins.

W. Nadler, A. T. Brünger, K. Schulten, M. Karplus

Research output: Contribution to journalArticlepeer-review


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 Mössbauer spectroscopic data.

Original languageEnglish (US)
Pages (from-to)7933-7937
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number22
StatePublished - Nov 1987
Externally publishedYes

ASJC Scopus subject areas

  • General


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