On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
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DOI：
10.1063/1.1472510
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发表时间：
2002-05-22
影响因子：
4.4
通讯作者：
Takada, S
中科院分区：
文献类型：
--
作者：
Fukunishi, H;Watanabe, O;Takada, S
受蛋白质结构预测问题的启发，我们开发了两种用于高效配置采样的汉密尔顿副本交换方法（REM）变体，（1）缩放疏水性REM和（2）幻影链REM，并将其性能与普通REM进行比较。首先指出了普通REM在应用于生物分子等大系统时存在的不足，而Hamilton REM（Hamiltonian REM）可以弥补这一不足，然后给出了两个适用于粗粒蛋白质模型的Hamilton REM的例子. (1)缩放的疏水性REM制备以疏水相互作用的各种强度为特征的复制品。模拟水溶液环境的最强相互作用使蛋白质折叠，而弱疏水性使蛋白质在有机溶剂中展开。这些环境之间的交换使蛋白质能够从错误折叠的陷阱中逃脱，并加速构象搜索。这类似于帮助蛋白质在体内折叠的分子伴侣的作用。(2)幻影链REM使用允许不同程度的原子重叠的副本。通过允许一些复制品中的原子重叠，肽链可以自身交叉，这可以加速构象采样。使用我们开发的粗获得的模型，我们计算平衡概率分布的聚丙氨酸16聚体和一个小的蛋白质，这些REM和比较的准确性的结果。我们看到，缩放的疏水性REM是最有效的方法中的三个REM研究。(C)2002年美国物理学会。
Motivated by the protein structure prediction problem, we develop two variants of the Hamiltonian replica exchange methods (REMs) for efficient configuration sampling, (1) the scaled hydrophobicity REM and (2) the phantom chain REM, and compare their performance with the ordinary REM. We first point out that the ordinary REM has a shortage for the application to large systems such as biomolecules and that the Hamiltonian REM, an alternative formulation of the REM, can give a remedy for it. We then propose two examples of the Hamiltonian REM that are suitable for a coarse-grained protein model. (1) The scaled hydrophobicity REM prepares replicas that are characterized by various strengths of hydrophobic interaction. The strongest interaction that mimics aqueous solution environment makes proteins folding, while weakened hydrophobicity unfolds proteins as in organic solvent. Exchange between these environments enables proteins to escape from misfolded traps and accelerate conformational search. This resembles the roles of molecular chaperone that assist proteins to fold in vivo. (2) The phantom chain REM uses replicas that allow various degrees of atomic overlaps. By allowing atomic overlap in some of replicas, the peptide chain can cross over itself, which can accelerate conformation sampling. Using a coarse-gained model we developed, we compute equilibrium probability distributions for poly-alanine 16-mer and for a small protein by these REMs and compare the accuracy of the results. We see that the scaled hydrophobicity REM is the most efficient method among the three REMs studied. (C) 2002 American Institute of Physics.