Peptide Folding Kinetics from Replica Exchange Molecular Dynamics

Details Peptide Folding Kinetics from Replica Exchange Molecular Dynamics Peptide Folding Kinetics from Replica Exchange Molecular Dynamics

2007-10-29

arxiv.org/abs/0710.5533v2

Phys. Rev. E 77 (3), 030902(R) (2008)

Physics

Condensed Matter

Soft Condensed Matter

4 pages, 4 figures; v2: updated abstract and Fig. 3

Scientific paper

10.1103/PhysRevE.77.030902

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 ~1/(100 ns) to ~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.

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