Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions.
Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions.
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DOI：
10.1021/ct400751u
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发表时间：
2014-01-14
影响因子：
5.5
通讯作者：
Merz, Kenneth M., Jr.
中科院分区：
文献类型：
--
作者：
Li, Pengfei;Merz, Kenneth M., Jr.
在蛋白质数据库中，金属离子存在于几乎一半的蛋白质中，它们在生物体的代谢过程中充当结构、电子传递和催化元素。分子动力学（MD）模拟是一个强大的工具，提供有关生物分子系统在原子水平上的信息。再加上计算能力的增长，像粒子网格埃瓦尔德（PME）方法的算法已经成为公认的标准时，处理长距离相互作用的MD模拟。金属离子的非键模型由静电势加上12-6的Lennard Jones（LJ）势组成，由于其相对于更精确的模型的速度而被广泛使用。在以前的工作中，我们发现，不存在理想的参数，再现几个实验性质的M（II）离子同时使用非键模型加上PME方法由于低估的金属离子-配体相互作用。通过考虑非键模型的性质，我们提出，所观察到的误差主要来自忽略电荷诱导偶极相互作用。静电加12-6 LJ势模型对于中性系统相当有效，但对于更高电荷的系统却很困难。在目前的工作中，我们设计和参数化一个新的非键模型的金属离子通过添加1/r4项的12-6模型。我们称之为12-6-4 LJ型非键模型，因为它的数学结构。确定TIP 3 P、SPC/E和TIP 4PEW水模型的16 + 2金属离子的参数。最后的参数重现实验水合自由能（HFE），离子-氧距离（IOD）在第一溶剂化壳层和配位数（CN）准确的金属离子的调查。在不同浓度的MgCl 2水溶液和Mg 2 +-核酸系统中的初步测试显示了合理的结果，表明本参数可以在混合系统中工作。12-6-4 LJ型非键模型很容易被采用到标准力场，如AMBER，CHARMM和OPLS-AA，只有一个适度的计算开销。新的非键合模型不考虑电荷转移效应明确，因此，可能不适合模拟系统的电荷转移效应起决定性作用。
Metal ions exist in almost half of the proteins in the protein databank and they serve as structural, electron-transfer and catalytic elements in the metabolic processes of organisms. Molecular Dynamics (MD) simulation is a powerful tool that provides information about biomolecular systems at the atomic level. Coupled with the growth in computing power, algorithms like the Particle Mesh Ewald (PME) method have become the accepted standard when dealing with long-range interactions in MD simulations. The nonbonded model of metal ions consists of an electrostatic plus 12-6 Lennard Jones (LJ) potential and is used largely because of its speed relative to more accurate models. In previous work we found that ideal parameters do not exist that reproduce several experimental properties for M(II) ions simultaneously using the nonbonded model coupled with the PME method due to the underestimation of metal ion-ligand interactions. Via a consideration of the nature of the nonbonded model, we proposed that the observed error largely arises from overlooking charge-induced dipole interactions. The electrostatic plus 12-6 LJ potential model works reasonably well for neutral systems but does struggle with more highly charged systems. In the present work we designed and parameterized a new nonbonded model for metal ions by adding a 1/r4 term to the 12-6 model. We call it the 12-6-4 LJ-type nonbonded model due to its mathematical construction. Parameters were determined for 16 +2 metal ions for the TIP3P, SPC/E and TIP4PEW water models. The final parameters reproduce the experimental hydration free energies (HFE), ion-oxygen distances (IOD) in the first solvation shell and coordination numbers (CN) accurately for the metal ions investigated. Preliminary tests on MgCl2 at different concentrations in aqueous solution and Mg2+--nucleic acid systems show reasonable results suggesting that the present parameters can work in mixed systems. The 12-6-4 LJ-type nonbonded model is readily adopted into standard force fields like AMBER, CHARMM and OPLS-AA with only a modest computational overhead. The new nonbonded model doesn’t consider charge-transfer effects explicitly and, hence, may not suitable for the simulation of systems where charge-transfer effects play a decisive role.
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影响因子：
2.8
作者：
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通讯作者：
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作者：
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