pH-Replica Exchange Molecular Dynamics In Proteins Using A Discrete Protonation Method

摘要: Protonation equilibria in biological molecules modulates structure, dynamics, and function. A pH-replica exchange molecular dynamics (pH-REMD) method is described here to improve the coupling between conformational protonation sampling. Under a Hamiltonian replica setup, conformations are swapped two neighboring replicas, which themselves at different pHs. The has been validated on series of systems. We applied pH-REMD model compounds, an terminally charged ADFDA pentapeptide, heptapeptide derived from ovomucoid third domain (OMTKY3). In all those systems, predicted pKa by very close experimental value almost identical ones obtained constant pH (CpH MD). presented here, pH-REMD, advantage faster convergence properties due enhanced sampling both conformation spaces.