使用三种流行的水模型获得的 DNA 周围 Na+ 和 K+ 分布的异同,Journal of Chemical Theory and Computation

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使用三种流行的水模型获得的 DNA 周围 Na+ 和 K+ 分布的异同
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2021-10-11 , DOI: 10.1021/acs.jctc.1c00332
Egor S Kolesnikov ₁ , Ivan Yu Gushchin ₁ , Petr A Zhilyaev ₂ , Alexey V Onufriev _{3,

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Affiliation

我们比较了双链 DNA 周围钠离子和钾离子的分布，使用固定电荷 SPC/E、TIP3P 和 OPC 水模型和 Joung/Cheatham (J/C) 离子参数集以及 Li/Merz 进行模拟OPC 水的 HFE 6–12 (L/M HFE) 离子参数。在所有模拟中，离子分布与曼宁凝聚理论和德拜-休克尔理论在质量上一致，符合预期。与实验一致，单价离子与 DNA 的结合亲和力并不取决于每种溶剂模型中的离子类型。然而，深度结合离子（包括结合到特定位点的离子）的行为很大程度上取决于溶剂模型。特别是，AT 束小沟中钾离子的数量在测试的溶剂模型之间至少相差 3 倍。与DNA相关的钠离子数量与OPC水模型的实验定量一致，紧随其后的是TIP3P+J/C；SPC/E+J/C 与实验的最大偏差约为 10%。另一方面，SPC/E+J/C 模型与实验钾结合位点最为一致（67%），其次是 OPC+J/C（60%）、TIP3P+J/C（53%）和OPC+L/M HFE (27%)。采用TIP3P+J/C进行NBFIX校正提高了其与实验的一致性。总之，溶剂模型的选择对于模拟 DNA 周围钠离子和钾离子的扩散气氛影响不大，但离子分布对螺旋轴附近的溶剂模型变得越来越敏感。我们对这些趋势提供了解释。没有单一的金标准溶剂模型，

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Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models

We have compared distributions of sodium and potassium ions around double-stranded DNA, simulated using fixed charge SPC/E, TIP3P, and OPC water models and the Joung/Cheatham (J/C) ion parameter set, as well as the Li/Merz HFE 6–12 (L/M HFE) ion parameters for OPC water. In all the simulations, the ion distributions are in qualitative agreement with Manning’s condensation theory and the Debye–Hückel theory, where expected. In agreement with experiment, binding affinity of monovalent ions to DNA does not depend on ion type in every solvent model. However, behavior of deeply bound ions, including ions bound to specific sites, depends strongly on the solvent model. In particular, the number of potassium ions in the minor groove of AT-tracts differs at least 3-fold between the solvent models tested. The number of sodium ions associated with the DNA agrees quantitatively with the experiment for the OPC water model, followed closely by TIP3P+J/C; the largest deviation from the experiment, ∼10%, is seen for SPC/E+J/C. On the other hand, SPC/E+J/C model is most consistent (67%) with the experimental potassium binding sites, followed by OPC+J/C (60%), TIP3P+J/C (53%), and OPC+L/M HFE (27%). The use of NBFIX correction with TIP3P+J/C improves its consistency with the experiment. In summary, the choice of the solvent model matters little for simulating the diffuse atmosphere of sodium and potassium ions around DNA, but ion distributions become increasingly sensitive to the solvent model near the helical axis. We offer an explanation for these trends. There is no single gold standard solvent model, although OPC water with J/C ions or TIP3P with J/C + NBFIX may offer an imperfect compromise for practical simulations of ionic atmospheres around DNA.

更新日期：2021-11-09

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