Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?
Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?
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DOI：
10.1021/ct100379f
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发表时间：
2010-12-01
影响因子：
5.5
通讯作者：
Pantano, Sergio
中科院分区：
文献类型：
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作者：
Darre, Leonardo;Machado, Matias R.;Pantano, Sergio
生物过程发生在完全原子模拟通常无法达到的空间和时间尺度上。因此，经常使用简化或粗粒（CG）模型来进行这些系统的理论研究。在这种背景下，溶剂化性质的准确描述仍然是一个重要且具有挑战性的领域。在目前的工作中，我们报告了一种基于纯水中观察到的瞬态四面体结构的新 CG 模型。我们的代表将大约 11 个 WATer 分子集中到四个四面体互连的珠子中，因此命名为 WAT FOUR (WT4)。每个珠子都带有部分电荷，使模型能够明确考虑长程静电，产生自己的介电常数并消除均匀介电常数的缺点。我们获得了 278 至 328 K 范围内大多数生物相关温度条件下水环境的良好表示。该模型应用于溶剂化本工作中开发的简单 CG 电解质（Na+、K+ 和 Cl-）以及最近发表的核酸的简化表示。在这两种情况下，我们都获得了实验数据和原子模拟的良好相似性。特别是，DNA周围的溶剂化结构、抗衡离子的部分电荷中和、钠优于钾的偏好以及X射线晶体学报道的离子介导的小沟变窄都可以通过本方案很好地再现。这里提出的参数集开启了达到数微秒时间尺度的可能性，包括显式溶剂化、离子特异性和长程静电，保持近原子分辨率并显着降低计算成本。
Biological processes occur on space and time scales that are often unreachable for fully atomistic simulations. Therefore, simplified or coarse grain (CG) models for the theoretical study of these systems are frequently used. In this context, the accurate description of solvation properties remains an important and challenging field. In the present work, we report a new CG model based on the transient tetrahedral structures observed in pure water. Our representation lumps approximately 11 WATer molecules into FOUR tetrahedrally interconnected beads, hence the name WAT FOUR (WT4). Each bead carries a partial charge allowing the model to explicitly consider long-range electrostatics, generating its own dielectric permittivity and obviating the shortcomings of a uniform dielectric constant. We obtained a good representation of the aqueous environment for most biologically relevant temperature conditions in the range from 278 to 328 K. The model is applied to solvate simple CG electrolytes developed in this work (Na+, K+, and Cl-) and a recently published simplified representation of nucleic acids. In both cases, we obtained a good resemblance of experimental data and atomistic simulations. In particular, the solvation structure around DNA, partial charge neutralization by counterions, preference for sodium over potassium, and ion mediated minor groove narrowing as reported from X-ray crystallography are well reproduced by the present scheme. The set of parameters presented here opens the possibility of reaching the multimicroseconds time scale, including explicit solvation, ionic specificity, and long-range electrostatics, keeping nearly atomistic resolution with significantly reduced computational cost.