Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model
Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model
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DOI：
10.1021/jp907464b
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发表时间：
2010-03-11
影响因子：
3.3
通讯作者：
Pietrucci, Fabio
中科院分区：
文献类型：
--
作者：
Cossio, Pilar;Marinelli, Fabrizio;Pietrucci, Fabio
生物分子中复杂构象转变的计算机模拟，如蛋白质折叠，被认为是计算化学的主要目标之一。最近发展起来的一种方法--偏置交换金属吸附法成功地用于可逆折叠一些小的球状蛋白质。这项工作的目的是进一步改善这种有前途的技术。这是通过使用粗粒度力场UNRES搜索最佳参数集来实现的，这些参数集能够在尽可能短的时间内折叠48个氨基酸的蛋白质1 E0 G。结果表明，偏置交换元自相关，如果适当优化，允许找到折叠状态的1 E0 G显着快于正常的副本交换。
Computer simulation of complex conformational transitions in biomolecules, Such as protein folding, is considered one of the main goals of computational chemistry. A recently developed methodology, bias-exchange metadynamics, was Successfully Used to reversibly fold some small globular proteins. The objective of this work is to further improve this promising technique. This is accomplished by searching for the optimal set of parameters that enable folding a 48 amino acid protein, 1E0G, in the shortest possible time, using a coarse-grained force field UNRES. It is shown that bias-exchange metadynamics, if appropriately optimized, allows finding the folded state of 1E0G significantly faster than normal replica exchange.