Identifying and correcting non-Markov states in peptide conformational dynamics

Nerukh, Dmitry, Jensen, Christian H. and Glen, Robert C. (2010). Identifying and correcting non-Markov states in peptide conformational dynamics. Journal of Chemical Physics, 132 (8), 084104.

Abstract

Conformational transitions in proteins define their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We test this assumption by analyzing the transitions obtained directly from the dynamics of a molecular dynamics simulated peptide valine-proline-alanine-leucine and states defined phenomenologically using clustering in dihedral space. We find that the transitions are Markovian at the time scale of ˜ 50 ps and longer. However, at the time scale of 30–40 ps the dynamics loses its Markov property. Our methodology reveals the mechanism that leads to non-Markov behavior. It also provides a way of regrouping the conformations into new states that now possess the required Markov property of their dynamics.

Publication DOI: https://doi.org/10.1063/1.3328781
Divisions: Engineering & Applied Sciences > Mathematics
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Additional Information: Copyright 2010 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Nerukh, Dmitry; Jensen, Christian H. and Glen, Robert C. (2010). Identifying and correcting non-Markov states in peptide conformational dynamics. Journal of Chemical Physics, 132 (8), 084104 and may be found at http://link.aip.org/link/?JCP/132/084104/1
Uncontrolled Keywords: Markov processes,molecular biophysics,molecular configurations,molecular dynamics method,proteins,Physical and Theoretical Chemistry,Medicine(all),Physics and Astronomy(all)
Full Text Link: http://link.aip ... CP/132/084104/1
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
Published Date: 2010
Authors: Nerukh, Dmitry ( 0000-0001-9005-9919)
Jensen, Christian H.
Glen, Robert C.

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