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Anders Irbäck. Photo.

Anders Irbäck

Professor

Anders Irbäck. Photo.

Accelerating atomic-level protein simulations by flat-histogram techniques.

Author

  • Sigurdur Jonsson
  • Sandipan Mohanty
  • Anders Irbäck

Summary, in English

Flat-histogram techniques provide a powerful approach to the simulation of first-order-like phase transitions and are potentially very useful for protein studies. Here, we test this approach by implicit solvent all-atom Monte Carlo (MC) simulations of peptide aggregation, for a 7-residue fragment (GIIFNEQ) of the Cu/Zn superoxide dismutase 1 protein (SOD1). In simulations with 8 chains, we observe two distinct aggregated/non-aggregated phases. At the midpoint temperature, these phases coexist, separated by a free-energy barrier of height 2.7 k(B)T. We show that this system can be successfully studied by carefully implemented flat-histogram techniques. The frequency of barrier crossing, which is low in conventional canonical simulations, can be increased by turning to a two-step procedure based on the Wang-Landau and multicanonical algorithms.

Department/s

  • Computational Biology and Biological Physics
  • MultiPark: Multidisciplinary research focused on Parkinson´s disease

Publishing year

2011

Language

English

Publication/Series

Journal of Chemical Physics

Volume

135

Issue

12

Document type

Journal article

Publisher

American Institute of Physics (AIP)

Topic

  • Biophysics

Status

Published

ISBN/ISSN/Other

  • ISSN: 0021-9606