Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins.
Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins.
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DOI：
10.1016/j.bbapap.2012.12.016
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发表时间：
2013-05
期刊：
影响因子：
--
通讯作者：
Katja Ostermeir;M. Zacharias
中科院分区：
文献类型：
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作者：
Katja Ostermeir;M. Zacharias
分子动力学(MD)模拟非常适合在高空间(原子)和高时间分辨率下同时研究蛋白质和多肽的可塑性和灵活性。然而，其适用性仍然受到力场精度和当前MD模拟中常规所能达到的最大模拟时间的限制。为了提高采样质量，副本交换(Replica-Exchange，REMD)方法已经成为一种流行的方法，是目前应用最广泛的高级采样方法。REMD方法的许多变体已被设计为减少计算需求或加强沿特定构象变量集的采样。将概述最近的方法学进展，并讨论这些方法的具体目标和优点。还将讨论在自由能模拟和内在无序的多肽和蛋白质的高级采样方面的应用。本文是一期特刊的一部分，题为：蛋白质的新兴动态观点：蛋白质在变构、进化和自组装中的可塑性。
Molecular dynamics (MD) simulations are ideally suited to investigate protein and peptide plasticity and flexibility simultaneously at high spatial (atomic) and high time resolution. However, the applicability is still limited by the force field accuracy and by the maximum simulation time that can be routinely achieved in current MD simulations. In order to improve the sampling the replica-exchange (REMD) methodology has become popular and is now the most widely applied advanced sampling approach. Many variants of the REMD method have been designed to reduce the computational demand or to enhance sampling along specific sets of conformational variables. An overview on recent methodological advances and discussion of specific aims and advantages of the approaches will be given. Applications in the area of free energy simulations and advanced sampling of intrinsically disordered peptides and proteins will also be discussed. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.