Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

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

Jonsson, Sigurdur LU ; Mohanty, Sandipan and Irbäck, Anders LU orcid (2011) In Journal of Chemical Physics 135(12).
Abstract
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,... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
135
issue
12
article number
125102
publisher
American Institute of Physics (AIP)
external identifiers
  • wos:000295619700058
  • pmid:21974561
  • scopus:80053501774
ISSN
0021-9606
DOI
10.1063/1.3643328
language
English
LU publication?
yes
id
95d9206a-b48f-4d8c-a258-22bf0272b9f2 (old id 2200791)
date added to LUP
2016-04-01 10:51:10
date last changed
2021-06-08 04:12:05
@article{95d9206a-b48f-4d8c-a258-22bf0272b9f2,
  abstract     = {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.},
  author       = {Jonsson, Sigurdur and Mohanty, Sandipan and Irbäck, Anders},
  issn         = {0021-9606},
  language     = {eng},
  number       = {12},
  publisher    = {American Institute of Physics (AIP)},
  series       = {Journal of Chemical Physics},
  title        = {Accelerating atomic-level protein simulations by flat-histogram techniques.},
  url          = {http://dx.doi.org/10.1063/1.3643328},
  doi          = {10.1063/1.3643328},
  volume       = {135},
  year         = {2011},
}