Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation.
Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation.
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DOI：
10.1063/1.4812839
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发表时间：
2013-07
期刊：
影响因子：
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通讯作者：
Yanxiang Zhao;Y. Kwan;Jianwei Che;Bo Li;J. McCammon
中科院分区：
文献类型：
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作者：
Yanxiang Zhao;Y. Kwan;Jianwei Che;Bo Li;J. McCammon
提出了一种求解带电分子溶剂化的相场变分隐式溶剂方法。这种方法的起点是用相场表示溶质-溶剂界面，相场在溶质区取一个值，在溶剂区取另一个值，在一个小的过渡层上从一个到另一个平滑过渡。所有可能相场的有效自由能泛函的最小化决定了基本分子系统的平衡构象和自由能。所有表面能、溶质-溶剂范德华相互作用和静电相互作用通过相场自洽耦合在一起。表面能来源于双势垒势的最小化和场的梯度。静电相互作用用库仑场近似来描述。设计和实现了精确和有效的方法来数值地松弛潜在的带电分子系统。对单离子、双板系统和双域蛋白质的应用表明，新的理论和方法可以捕捉到疏水约束下的毛细蒸发和相应的分子动力学模拟中的多个平衡态。讨论了相场方法和原始的尖界面变分方法的比较。
A phase-field variational implicit-solvent approach is developed for the solvation of charged molecules. The starting point of such an approach is the representation of a solute-solvent interface by a phase field that takes one value in the solute region and another in the solvent region, with a smooth transition from one to the other on a small transition layer. The minimization of an effective free-energy functional of all possible phase fields determines the equilibrium conformations and free energies of an underlying molecular system. All the surface energy, the solute-solvent van der Waals interaction, and the electrostatic interaction are coupled together self-consistently through a phase field. The surface energy results from the minimization of a double-well potential and the gradient of a field. The electrostatic interaction is described by the Coulomb-field approximation. Accurate and efficient methods are designed and implemented to numerically relax an underlying charged molecular system. Applications to single ions, a two-plate system, and a two-domain protein reveal that the new theory and methods can capture capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics simulations. Comparisons of the phase-field and the original sharp-interface variational approaches are discussed.