Coarse master equations for Peptide folding dynamics.

Coarse master equations for Peptide folding dynamics. Research Abstract Details 

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Coarse master equations for Peptide folding dynamics. Abstract Text:

We construct coarse master equations for peptide folding dynamics from atomistic molecular dynamics simulations. A maximum-likelihood propagator-based method allows us to extract accurate rates for the transitions between the different conformational states of the small helix-forming peptide Ala5. Assigning the conformational states by using transition paths instead of instantaneous molecular coordinates suppresses the effects of fast non-Markovian dynamics. The resulting master equations are validated by comparing their analytical correlation functions with those obtained directly from the molecular dynamics simulations. We find that the master equations properly capture the character and relaxation times of the entire spectrum of conformational relaxation processes. By using the eigenvectors of the transition rate matrix, we are able to systematically coarse-grain the system. We find that a two-state description, with a folded and an unfolded state, roughly captures the slow conformational dynamics. A four-state model, with two folded and two unfolded states, accurately recovers the three slowest relaxation process with time scales between 1.5 and 7 ns. The master equation models not only give access to the slow conformational dynamics but also shed light on the molecular mechanisms of the helix-coil transition.

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Coarse master equations for Peptide folding dynamics. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: The journal of physical chemistry. B

VOLUME: 112

Page Numbers: 6057-69

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ISSN: 1520-6106

DAY: 31

MONTH: 01

YEAR: 2008

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LANGUAGE: eng

NlmUniqueID: 101157530

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Grant and Affiliation Information for Coarse master equations for Peptide folding dynamics.

AFFILIATION: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520.

Country: United States

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MEDLINETA: J Phys Chem B

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