Peptide folding kinetics from replica exchange molecular dynamics.

Peptide folding kinetics from replica exchange molecular dynamics. Research Abstract Details 

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Peptide folding kinetics from replica exchange molecular dynamics. Abstract Text:

We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the approximately 1(100 ns) to approximately 1(1 ns) range can be obtained from REMD with exchange times of 5 ps , in excellent agreement with results from long equilibrium molecular dynamics.

Peptide folding kinetics from replica exchange molecular dynamics. Publishing Authors By Initials

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Peptide folding kinetics from replica exchange molecular dynamics. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Intr

Journal: Physical review. E, Statistical, nonlinear, and so

VOLUME: 77

Page Numbers: 030902

Journal Abbreviation:

ISSN: 1539-3755

DAY: 24

MONTH: 03

YEAR: 2008

Peptide folding kinetics from replica exchange molecular dynamics. Information

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LANGUAGE: eng

NlmUniqueID: 101136452

Peptide folding kinetics from replica exchange molecular dynamics. Keywords Mesh Terms:

KEYWORDS: Time Factors

MESH TERMS: chemistry

Chemical & Substance for Abstract: Peptide folding kinetics from replica exchange molecular dynamics. Information

Substance Name: Peptides

Registry Number: 0

Grant and Affiliation Information for Peptide folding kinetics from replica exchange molecular dynamics.

AFFILIATION: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892-0520, USA.

Country: United States

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MEDLINETA: Phys Rev E Stat Nonlin Soft Ma

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