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MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

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Xu, Yuanwei and Rodger, P. Mark (2017) MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation. Journal of Computational Physics, 333 . pp. 128-141. doi:10.1016/j.jcp.2016.12.016

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Official URL: http://dx.doi.org/10.1016/j.jcp.2016.12.016

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Abstract

We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.

Item Type: Journal Article
Subjects: Q Science > QC Physics
Q Science > QP Physiology
Divisions: Faculty of Science > Chemistry
Faculty of Science > Centre for Scientific Computing
Library of Congress Subject Headings (LCSH): Monte Carlo method , Lattice gauge theories, Proteins--Denaturation
Journal or Publication Title: Journal of Computational Physics
Publisher: Academic Press Inc. Elsevier Science
ISSN: 0021-9991
Official Date: 15 March 2017
Dates:
DateEvent
15 March 2017Published
15 December 2016Available
13 December 2016Accepted
14 March 2016Submitted
Date of first compliant deposit: 16 February 2017
Volume: 333
Page Range: pp. 128-141
DOI: 10.1016/j.jcp.2016.12.016
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
Funder: Engineering and Physical Sciences Research Council (EPSRC), University of Warwick. Centre for Scientific Computing
Grant number: ep-K000233 (EPSRC)

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