title: Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.
abstract: By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKapredictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model. The method involves standard molecular dynamics (MD) being propagated in explicit solvent followed by protonation state changes being attempted in GB implicit solvent at fixed intervals. Replica exchange along the pH-dimension (pH-REMD) helps to obtain acceptable titration behavior with the proposed method. We analyzed the effects of various parameters and settings on the titration behavior of CpHMD and pH-REMD in explicit solvent, including the size of the simulation unit cell and the length of the relaxation dynamics following protonation state changes. We tested the method with the amino acid model compounds, a small pentapeptide with two titratable sites, and hen egg white lysozyme (HEWL). The proposed method yields superior predicted pKavalues for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent.
authors.affiliation: Quantum Theory Project, Chemistry Department, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Swails
authors.affiliation: BioMaPS Institute for Quantitative Biology, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States.
authors.forename: Darrin M
authors.initials: DM
authors.lastname: York
authors.affiliation: Quantum Theory Project, Chemistry Department, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg