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

Srinivasaraghavan Kannan, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

101 Scopus citations

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.

Original languageEnglish
Pages (from-to)697-706
Number of pages10
JournalProteins: Structure, Function and Bioinformatics
Volume66
Issue number3
DOIs
StatePublished - 15 Feb 2007
Externally publishedYes

Keywords

  • Conformational sampling
  • Molecular dynamics simulation
  • Peptide folding
  • Protein folding
  • Protein structure prediction

Fingerprint

Dive into the research topics of 'Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential'. Together they form a unique fingerprint.

Cite this