Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.

Full Abstract

During replica exchange molecular dynamics (RexMD) simulations, several replicas of a system are simulated at different temperatures in parallel allowing for exchange between replicas at frequent intervals. This technique allows significantly improved sampling of conformational space and is increasingly being used for structure prediction of peptides and proteins. A drawback of the standard temperature RexMD is the rapid increase of the replica number with increasing system size to cover a desired temperature range. In an effort to limit the number of replicas, a new Hamiltonian-RexMD method has been developed that is specifically designed to enhance the sampling of peptide and protein conformations by applying various levels of a backbone biasing potential for each replica run. The biasing potential lowers the barrier for backbone dihedral transitions and promotes enhanced peptide backbone transitions along the replica coordinate. The application on several peptide cases including in all cases explicit solvent indicates significantly improved conformational sampling when compared with standard MD simulations. This was achieved with a very modest number of 5-7 replicas for each simulation system making it ideally suited for peptide and protein folding simulations as well as refinement of protein model structures in the presence of explicit solvent.2006 Wiley-Liss, Inc.

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Author information

Author/s: Kannan, Srinivasaraghavan (S); Zacharias, Martin (M);

Affiliation: School of Engineering and Science, International University Bremen, D-28759 Bremen, Germany.

Journal and publication information

Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Journal: Proteins (Proteins), published in United States. (Language: eng)

Reference: 2007-Feb; vol 66 (issue 3) : pp 697-706

Dates: Created 2007/01/16; Completed 2007/02/19;

PMID: 17120231, 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.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Molecular Conformation
Oligopeptides - chemistry
Peptides - chemistry
Protein Conformation
Proteins - chemistry
Threonine

Associated Chemicals: Dipeptides (0) ; Oligopeptides (0) ; Peptides (0) ; Proteins (0) ; chignolin (0) ; Alanine (56-41-7) ; Threonine (72-19-5)

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