文章基本信息

标题：Protein folding pathways from replica exchange simulations and a kinetic network model
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作者：Michael Andrec ; Anthony K. Felts ; Emilio Gallicchio 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2005
卷号：102
期号：19
页码：6801-6806
DOI：10.1073/pnas.0408970102
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：We present an approach to the study of protein folding that uses the combined power of replica exchange simulations and a network model for the kinetics. We carry out replica exchange simulations to generate a large ({approx}106) set of states with an all-atom effective potential function and construct a kinetic model for folding, using an ansatz that allows kinetic transitions between states based on structural similarity. We use this network to perform random walks in the state space and examine the overall network structure. Results are presented for the C-terminal peptide from the B1 domain of protein G. The kinetics is two-state after small temperature perturbations. However, the coil-to-hairpin folding is dominated by pathways that visit metastable helical conformations. We propose possible mechanisms for the {alpha}-helix/{beta}-hairpin interconversion.
关键词：graph ; master equation ; protein G