Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model.
Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model.
复制标题
自组装二肽：包括粗粒度模型中的溶剂自由度。
DOI：
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复制
发表时间：
2009
期刊：
影响因子：
--
通讯作者：
C. Peter
中科院分区：
文献类型：
--
作者：
A. Villa;N. V. D. van der Vegt;C. Peter
在上一篇论文[A.维拉角Peter，N. F. A.货车，物理化学物理，2009年，DOI：]，一个策略，以开发一个无溶剂的粗粒度模型的肽概述了它是基于原子（力场）的描述。粗粒度模型的设计，使它正确地捕捉分子的构象灵活性，并再现在水溶液中的肽之间的相互作用。在本文中，我们重新审视这个模型，并提出了一种方法来设计非键合的相互作用，这样也粗粒度的水平保持明确的溶剂自由度。在这种新方法中，我们依赖于基于结构的粗粒化方法，该方法保留了肽周围的溶剂化结构，并结合一种方法来设计肽珠之间的非键合电位，以正确地表示水中的肽-肽相互作用，并导致正确的热力学缔合行为。概述粗粒化策略为我们提供了两个（一个隐式和一个显式溶剂）模型，非常适合多尺度模拟和规模桥接的目的。我们表明，这是一个强大的工具，有效地模拟长时间尺度和大长度尺度的生物分子过程，如肽自组装。结合一个有效的backmapping方法，我们可以得到很好的平衡原子结构的聚集体。
In the previous paper [A. Villa, C. Peter, N. F. A. van der Vegt, Phys. Chem. Chem. Phys., 2009, DOI: ], a strategy to develop a solvent-free coarse-grained model for peptides is outlined which is based on an atomistic (force field) description. The coarse-grained model is designed such that it correctly captures the conformational flexibility of the molecules and reproduces the interaction between peptides in aqueous solution. In the present paper, we revisit this model and present a method to devise nonbonded interactions such that also the coarse-grained level maintains explicit solvent degrees of freedom. In this new approach we rely on a structure-based coarse graining methodology which preserves the solvation structure around the peptides in combination with a method to devise nonbonded potentials between peptide beads in a way that the peptide-peptide interaction in water is represented correctly and that results in the correct thermodynamic association behavior. The outlined coarse graining strategy provides us with two (one implicit- and one explicit-solvent) models that are well suited for multiscale-simulation and scale-bridging purposes. We show that this is a powerful tool to efficiently simulate long time-scale and large length-scale biomolecular processes such as peptide self-assembly. In combination with an efficient backmapping methodology we can obtain well-equilibrated atomistic structures of the resulting aggregates.
DOI：
10.1073/pnas.0407273101
发表时间：
2004-11-16
影响因子：
11.1
作者：
Nguyen, HD;Hall, CK
通讯作者：
Hall, CK
DOI：
10.1073/pnas.0400352101
发表时间：
2004-03-30
影响因子：
11.1
作者：
Lopez, CF;Nielsen, SO;Klein, ML
通讯作者：
Klein, ML
影响因子：
6.8
作者：
Ayton, Gary S.;Noid, Will G.;Voth, Gregory A.
通讯作者：
Voth, Gregory A.