pH replica‐exchange method based on discrete protonation states

Abstract

We propose a new algorithm for obtaining proton titration curves of ionizable residues. The algorithm is a pH replica-exchange method (PHREM) which is based on the constant pH algorithm of Mongan et al. [1]. In the original replica-exchange method, simulations of different replicas are performed at different temperature, and the temperatures are exchanged between the replicas. In our pH replica-exchange method, simulations of different replicas are performed at different pH values, and the pHs are exchanged between the replicas. The PHREM was applied to a blocked amino acid and to two protein systems (Snake Cardiotoxin and Turkey Ovomucoid Third Domain), in conjunction with a generalized Born implicit solvent. The performance and accuracy of this algorithm and the original constant pH method (PHMD) were compared. For a single set of simulations at different pHs, the use of PHREM yields more accurate Hill coefficients of titratable residues. By performing multiple sets of constant pH simulations started with different initial states the accuracy of predicted pKa values and Hill coefficients obtained with PHREM and PHMD methods becomes comparable. However, the PHREM algorithm exhibits better samplings of the protonation states of titratable residues and less scatter of the titration points and thus better precision of measured pKa values and Hill coefficients. In addition, PHREM exhibits faster convergence of individual simulations than the original constant pH algorithm.

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Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations

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pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method

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