Replica exchange molecular dynamics method for protein folding simulation.

Full Abstract

Understanding protein folding is one of the most challenging problems remaining in molecular biology. In this chapter, a highly parallel replica exchange molecular dynamics (REMD) method and its application to protein folding are described. The REMD method couples molecular dynamics trajectories with a temperature exchange Monte Carlo process for efficient sampling of the conformational space. A series of replicas are run in parallel at temperatures ranging from the desired temperature to a high temperature at which the replica can easily surmount the energy barriers. From time to time the configurations of neighboring replicas are exchanged and this exchange is accepted or rejected based on a Metropolis acceptance criterion that guarantees the detailed balance. Two example protein systems, one alpha-helix and one beta-hairpin, are used as case studies to demonstrate the power of the algorithm. Up to 64 replicas of solvated protein systems are simulated in parallel over a wide range of temperatures. The simulation results show that the combined trajectories in temperature and configurational space allow a replica to overcome free energy barriers present at low temperatures. These large-scale simulations also reveal detailed results on folding mechanisms, intermediate state structures, thermodynamic properties, and the temperature dependences for both protein systems.

Learn Faster Today Improve your study skills

Author information

Author/s: Zhou, Ruhong (R);

Affiliation: Department of Chemistry, Columbia University, New York, NY, USA.

Journal and publication information

Publication Type: Comparative Study; Journal Article

Journal: Methods in molecular biology (Clifton, N.J.) (Methods Mol Biol), published in United States. (Language: eng)

Reference: 2007-; vol 350 (issue ) : pp 205-23

Dates: Created 2006/09/07; Completed 2006/11/20;

PMID: 16957325, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

External Links for this article (including full text providers, if available):

Click Electronic Full-text Provider Links to see options for finding the electronic full text links to this article. Note there may be a subscription or fee required for access to the full text. See our FAQ for information on finding FREE full text articles.

This article may also be located in paper journal collections available in many libraries. Use the Journal and Publication Information above to find the full article.

MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Associated Chemicals: Proteins (0)

These are the highest related articles currently in the database:

See 100+ related articles.