Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.
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DOI：
10.1016/j.bbamem.2015.12.032
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发表时间：
2016-07
期刊：
影响因子：
--
通讯作者：
Sugita Y
中科院分区：
文献类型：
--
作者：
Mori T;Miyashita N;Im W;Feig M;Sugita Y
本文综述了各种增强的构象采样方法和显式/隐式溶剂/膜模型，以及它们在膜和膜蛋白结构和动力学研究中的最新应用。分子动力学模拟已成为研究生物学问题的重要工具，其成功依赖于适当的分子模型和有效的构象采样方法。考虑到计算成本和模拟精度之间的平衡，溶剂/膜环境的隐式表示是对显式全原子模型的合理逼近。隐式模型可以很容易地与复制交换分子动力学方法相结合，以探索更广泛的蛋白质构象空间。还简要讨论了其他分子模型和增强的构象采样方法。作为应用实例，介绍了近年来糖蛋白A、磷蛋白、淀粉样前体蛋白和混合脂质双分子层的模拟研究，并讨论了每种模拟模型和方法的准确性和效率。这篇文章是《膜蛋白》特刊的一部分。特邀编辑：J.C. Gumbart和Sergei Noskov。
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov.