Journal Article

PreJuSER-17850

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Accelerating atomic-level protein simulations by flat-histogram techniques

Jónsson, S. ; Mohanty, S.FZJ* ; Irbäck, A.

2011
American Institute of Physics Melville, NY

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Please use a persistent id in citations: http://hdl.handle.net/2128/7353  doi:10.1063/1.3643328

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.

Keyword(s): Molecular Dynamics Simulation (MeSH) ; Monte Carlo Method (MeSH) ; Superoxide Dismutase: chemistry (MeSH) ; Superoxide Dismutase: metabolism (MeSH) ; superoxide dismutase 1 ; Superoxide Dismutase ; J

Note: The simulations were performed at the LUNARC facility, Lund University. This work was in part funded by the Swedish Research Council.

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Contributing Institute(s):

1. Jülich Supercomputing Centre (JSC)

Research Program(s):

1. Scientific Computing (FUEK411) (FUEK411)
2. 411 - Computational Science and Mathematical Methods (POF2-411) (POF2-411)

Appears in the scientific report 2011

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