Biophys J. 2013 Aug 20;105(4):L15-7. doi: 10.1016/j.bpj.2013.06.036.
Recent development of titratable coions has paved the way for realizing all-atom molecular dynamics at constant pH. To further improve physical realism, here we describe a technique in which proton titration of the solute is directly coupled to the interconversion between water and hydroxide or hydronium. We test the new method in replica-exchange continuous constant pH molecular dynamics simulations of three proteins, HP36, BBL, and HEWL. The calculated pKa values based on 10-ns sampling per replica have the average absolute and root-mean-square errors of 0.7 and 0.9 pH units, respectively. Introducing titratable water in molecular dynamics offers a means to model proton exchange between solute and solvent, thus opening a door to gaining new insights into the intricate details of biological phenomena involving proton translocation.
可滴定离子的最新发展为实现恒 pH 值下的全原子分子动力学铺平了道路。为了进一步提高物理真实性，我们在这里描述了一种技术，其中溶质的质子滴定直接耦合到水和氢氧根或水合氢离子之间的相互转化。我们在三个蛋白质（HP36、BBL 和 HEWL）的 replica-exchange 连续恒 pH 分子动力学模拟中测试了新方法。基于每个 replica 10ns 采样的计算 pKa 值的平均绝对误差和均方根误差分别为 0.7 和 0.9 pH 单位。在分子动力学中引入可滴定水为模拟溶质和溶剂之间的质子交换提供了一种方法，从而为深入了解涉及质子转移的复杂生物现象提供了新的见解。
