Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

Katja Ostermeir, Martin Zacharias

Research output: Contribution to journalReview articlepeer-review

64 Scopus citations

Abstract

Molecular dynamics (MD) simulations are ideally suited to investigate protein and peptide plasticity and flexibility simultaneously at high spatial (atomic) and high time resolution. However, the applicability is still limited by the force field accuracy and by the maximum simulation time that can be routinely achieved in current MD simulations. In order to improve the sampling the replica-exchange (REMD) methodology has become popular and is now the most widely applied advanced sampling approach. Many variants of the REMD method have been designed to reduce the computational demand or to enhance sampling along specific sets of conformational variables. An overview on recent methodological advances and discussion of specific aims and advantages of the approaches will be given. Applications in the area of free energy simulations and advanced sampling of intrinsically disordered peptides and proteins will also be discussed. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.

Original languageEnglish
Pages (from-to)847-853
Number of pages7
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1834
Issue number5
DOIs
StatePublished - May 2013
Externally publishedYes

Keywords

  • Accelerated sampling
  • Conformational sampling
  • Force field calculation
  • Molecular dynamics simulation
  • Peptide and protein folding
  • Potential scaling

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