Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
Year: 2014
Type: article
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 pKa predictions 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 pKa values for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent.
DOI: 10.1021/ct401042b
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,500
Awards: PRAC - Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change, Collaborative Research SI2-SSE: Sustained Innovation in Acceleration of Molecular Dynamics on Future Computational Environments: Power to the People in the Cloud and on Accelerator, Computational Enzymology to Study Diverse Catalytic Strategies of RNA
OpenAlex ID: W2032427406