Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength.
Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength.
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生理溶液中的分子动力学：力场、碱金属离子和离子强度。
DOI：
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发表时间：
2010
影响因子：
5.5
通讯作者：
P. Carloni
中科院分区：
文献类型：
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作者：
Chao Zhang;S. Raugei;B. Eisenberg;P. Carloni
一价离子Na（+）、K（+）和Cl（-）存在于任何生物体中。含有这些离子的溶液的基本热力学性质被给出为在有限离子强度下单个离子的过量（电）化学势差。这个数量是许多生物过程的关键，包括膜离子通道中的离子渗透和DNA-蛋白质相互作用。它由与离子活性相关的化学贡献和与水/空气界面的伽伐尼电势相关的电贡献给出。在这里，我们研究分子动力学的基础上预测这些数量使用各种离子/水力场常用的生物模拟，即琥珀（新开发的），CHARMM，OPLS，Dang 95与TIP 3 P，SPC/E水。与实验进行了比较与相应的值的盐，其中数据是可用的。新开发的琥珀力场与TIP 3 P水的基础上的计算同意以及KCl和NaCl电解质在水溶液中的实验，如前所述。基于CHARMM-TIP 3 P和Dang 95-SPC/E力场的模拟结果分别与KCl和NaCl溶液的模拟结果吻合良好。其他模型不太准确。单阳离子过剩（电）化学势差原来是相似的所有力场考虑在这里。在KCl的情况下，计算出的电的贡献是一致的更高级别的计算。相反，与NaCl没有发现这样的协议。最后，我们发现，计算活动的单个Cl（-）离子原来明显依赖于类型的反式使用，与所有的力场调查。这些研究结果的生物分子系统的影响进行了讨论。
The monovalent ions Na(+) and K(+) and Cl(-) are present in any living organism. The fundamental thermodynamic properties of solutions containing such ions is given as the excess (electro-)chemical potential differences of single ions at finite ionic strength. This quantity is key for many biological processes, including ion permeation in membrane ion channels and DNA-protein interaction. It is given by a chemical contribution, related to the ion activity, and an electric contribution, related to the Galvani potential of the water/air interface. Here we investigate molecular dynamics based predictions of these quantities by using a variety of ion/water force fields commonly used in biological simulation, namely the AMBER (the newly developed), CHARMM, OPLS, Dang95 with TIP3P, and SPC/E water. Comparison with experiment is made with the corresponding values for salts, for which data are available. The calculations based on the newly developed AMBER force field with TIP3P water agrees well with experiment for both KCl and NaCl electrolytes in water solutions, as previously reported. The simulations based on the CHARMM-TIP3P and Dang95-SPC/E force fields agree well for the KCl and NaCl solutions, respectively. The other models are not as accurate. Single cations excess (electro-)chemical potential differences turn out to be similar for all the force fields considered here. In the case of KCl, the calculated electric contribution is consistent with higher level calculations. Instead, such agreement is not found with NaCl. Finally, we found that the calculated activities for single Cl(-) ions turn out to depend clearly on the type of counterion used, with all the force fields investigated. The implications of these findings for biomolecular systems are discussed.
影响因子：
4.4
作者：
Harder, Edward;Roux, Benoit
通讯作者：
Roux, Benoit