Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles
Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles
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DOI：
10.1002/jcc.23476
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发表时间：
2014-01
影响因子：
3
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
已经开发了一种哈密顿交换分子动力学（REMD）模拟方法，其采用二维主链和一维侧链偏置势，专门用于促进肽中的构象转变。为了最佳地利用副本框架，在模拟期间适当地调整每个副本中的偏置电位的水平。这导致了相邻副本之间的高交换率和每个副本中所有构象异构体的占用/流动的改善。在几种肽和蛋白质系统上测试了该方法的性能，并与常规MD模拟和以前的REMD研究进行了比较。观察到不受限制的蛋白质和肽折叠模拟以及环侧翼蛋白质区域的流动性受限的环结构的改进的相关构象状态的采样。© 2013 Wiley Periodicals，Inc.
A Hamiltonian Replica‐Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two‐dimensional backbone and one‐dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions. © 2013 Wiley Periodicals, Inc.