Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles

Katja Ostermeir, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.

Original languageEnglish
Pages (from-to)150-158
Number of pages9
JournalJournal of Computational Chemistry
Volume35
Issue number2
DOIs
StatePublished - 15 Jan 2014
Externally publishedYes

Keywords

  • accelerated sampling
  • conformational sampling
  • force field calculation
  • molecular dynamics simulations
  • peptide and protein folding
  • potential scaling

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