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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 ISSN 0021-9991.
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Official URL: http://dx.doi.org/10.1016/j.jcp.2016.12.016
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 | ||||||||||
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| Subjects: | Q Science > QC Physics Q Science > QP Physiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Chemistry Faculty of Science, Engineering and Medicine > Science > Centre for Scientific Computing |
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| 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: |
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| 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 (Creative Commons) | ||||||||||
| Date of first compliant deposit: | 16 February 2017 | ||||||||||
| Date of first compliant Open Access: | 15 December 2017 | ||||||||||
| Funder: | Engineering and Physical Sciences Research Council (EPSRC), University of Warwick. Centre for Scientific Computing | ||||||||||
| Grant number: | ep-K000233 (EPSRC) |
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