Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
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.
Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, 444-8585, Japan.
Satoru G
SG
Itoh
Hisashi
H
Okumura
D000409:Alanine / Q000737:chemistry*; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D010446:Peptide Fragments / Q000737:chemistry*
D016229:Amyloid beta-Peptides; D004151:Dipeptides; D010446:Peptide Fragments; C512364:beta-amyloid peptide (29-42); D000409:Alanine
Monte Carlo; amyloid; molecular dynamics; replica-exchange method; replica-permutation method