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

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• 作者：Yuanwei Xu^a ; ^{yuanwxu@warwickgrad.net} ; P. Mark Rodger^a ; ^b ; ^{p.m.rodger@warwick.ac.uk}
• 关键词：Lattice Monte Carlo ; Parallel tempering ; Multicanonical sampling ; Protein aggregation ; Twin-arginine translocation
• 刊名：Journal of Computational Physics
• 出版年：2017
• 出版时间：15 March 2017
• 年：2017
• 卷：333
• 期：Complete
• 页码：128-141
• 全文大小：716 K
• 卷排序：333

文摘

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.