Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.
复制标题
DOI：
10.1021/jp8001614
复制
发表时间：
2008-07-31
期刊：
影响因子：
--
通讯作者：
Cheatham TE 3rd
中科院分区：
文献类型：
--
作者：
Joung IS;Cheatham TE 3rd
碱(Li+、Na+、K+、Rb+和Cs+)和卤化物(F−、Cl−、Br−和I−)离子在许多生物现象中扮演着重要的角色，从稳定生物分子结构到影响生物分子动力学，再到对动态平衡和信号转导的关键生理影响。在生物分子结构、动力学、折叠、催化和功能的原子模拟中，为了正确地模拟离子相互作用和稳定性，一价离子的准确模型或表示是至关重要的。一个好的模型需要同时再现离子的许多性质，包括它们的结构、动力学、溶剂化，以及这些离子在晶体和溶液中相互作用以及离子与其他分子的相互作用。目前，生物分子的最佳力场采用简单的加性、不可极化、成对的原子相互作用势。在这项工作中，我们描述了我们在成对库仑和6-12 Lennard-Jones框架内建立更好的单价离子模型的努力，其中模型被调整以平衡Ewald模拟中的晶体和溶液性质，并选择特定的众所周知的水模型。尽管已经清楚地证明，真正准确地处理离子将需要包括非加性和极化性(特别是对于阴离子)，最终甚至需要量子力学处理，但我们的目标是简单地推动添加处理的极限，看看是否可以创建一个平衡的模型。所采用的方法是通用的，可以推广到其他离子和极化力场模型。我们的出发点集中在对生物分子在盐溶液中的长期模拟的观察，在琥珀力场中，盐晶体的形成远远低于它们的溶解极限。琥珀参数中伪影的可能原因与Smith和Dang氯化物参数与琥珀适应的äqvist阳离子参数的天真混合有关。为了提供更合适的平衡，我们重新优化了离子的Lennard-Jones势参数和特定的水模型选择。为了验证和优化这些参数，我们计算了溶剂化离子的水合自由能以及碱卤酸盐晶体的晶格能(LE)和晶格常数(LC)。这是第一次系统地扫描Lennard-Jones空间(深度和半径都很好)，同时平衡所有碱离子和卤化物离子对组合的离子性质，如LE和LC。整个单价系列的优化避免了系统性偏差。开发、优化和表征的离子参数针对一些最常用的刚性和非极化水模型，特别是TIP3P、TIP4PEW和SPC/E，除了很好地再现了溶液和晶体性质外，新的离子参数还很好地再现了离子与水的结合能和第一水化壳层的半径。
Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Åqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4PEW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells.
登录
查看更多内容
影响因子：
15
作者：
Brovchenko, Ivan;Krukau, Aliaksei;Mazur, Alexey K.
通讯作者：
Mazur, Alexey K.
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
4.4
作者：
Asthagiri, D;Pratt, LR;Ashbaugh, HS
通讯作者：
Ashbaugh, HS
影响因子：
4.4
作者：
BEGLOV, D;ROUX, B
通讯作者：
ROUX, B
影响因子：
5.7
作者：
Auffinger, P;Bielecki, L;Westhof, E
通讯作者：
Westhof, E