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J Phys Chem B. 2008 May 15;112(19):6083-93. doi: 10.1021/jp076377+. Epub 2008 Feb 6.

Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

Author information

1
Department of Physics and Astronomy, Rutgers, the State University of New Jersey, 136 Frelinghuysen Road, Piscataway, New Jersey 08854, USA.

Abstract

The efficiency of temperature replica exchange (RE) simulations hinge on their ability to enhance conformational sampling at physiological temperatures by taking advantage of more rapid conformational interconversions at higher temperatures. While temperature RE is a parallel simulation technique that is relatively straightforward to implement, kinetics in the RE ensemble is complicated, and there is much to learn about how best to employ RE simulations in computational biophysics. Protein folding rates often slow down above a certain temperature due to entropic bottlenecks. This "anti-Arrhenius" behavior represents a challenge for RE. However, it is far from straightforward to systematically explore the impact of this on RE by brute force molecular simulations, since RE simulations of protein folding are very difficult to converge. To understand some of the basic mechanisms that determine the efficiency of RE, it is useful to study simplified low dimensionality systems that share some of the key characteristics of molecular systems. Results are presented concerning the efficiency of temperature RE on a continuous two-dimensional potential that contains an entropic bottleneck. Optimal efficiency was obtained when the temperatures of the replicas did not exceed the temperature at which the harmonic mean of the folding and unfolding rates is maximized. This confirms a result we previously obtained using a discrete network model of RE. Comparison of the efficiencies obtained using the continuous and discrete models makes it possible to identify non-Markovian effects, which slow down equilibration of the RE ensemble on the more complex continuous potential. In particular, the rate of temperature diffusion and also the efficiency of RE is limited by the time scale of conformational rearrangements within free energy basins.

PMID:
18251533
PMCID:
PMC2978075
DOI:
10.1021/jp076377+
[Indexed for MEDLINE]
Free PMC Article

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