Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides

J Comput Chem. 2013 Nov 5;34(29):2493-7. doi: 10.1002/jcc.23402. Epub 2013 Aug 7.

Abstract

We propose the Hamiltonian replica-permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa-Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid-β(29-42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica-exchange method. We illustrate the protein misfolding funnel of amyloid-β(29-42) and reveal its dimerization pathways.

Keywords: Monte Carlo; amyloid; molecular dynamics; replica-exchange method; replica-permutation method.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alanine / chemistry*
  • Amyloid beta-Peptides / chemistry*
  • Dipeptides / chemistry*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Monte Carlo Method
  • Peptide Fragments / chemistry*

Substances

  • Amyloid beta-Peptides
  • Dipeptides
  • Peptide Fragments
  • beta-amyloid peptide (29-42)
  • Alanine