title: Introducing titratable water to all-atom molecular dynamics at constant pH.
abstract: 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.
authors: Wei
authors: W
authors: Chen
authors: Jason A
authors: JA
authors: Wallace
authors: Zhi
authors: Z
authors: Yue
authors: Jana K
authors: JK
authors: Shen
mesh_terms: D006863:Hydrogen-Ion Concentration; D006878:Hydroxides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009861:Onium Compounds / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D006878:Hydroxides; D009861:Onium Compounds; D011506:Proteins; D014867:Water; C027727:hydronium ion
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