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bioRxiv · 10.1101/2022.06.04.494833

GPU-Accelerated All-atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber

Harris, J. A.·Liu, R.·Martins de Oliveira, V.·Vazquez Montelongo, E.·Henderson, J. A.·Shen, J.
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Abstract

Constant pH molecular dynamics (MD) simulations sample protonation states on the fly according to the conformational environment and user specified pH condition; however, the current accuracy is limited due to the use of implicit-solvent models or a hybrid solvent scheme. Here we report the first GPU-accelerated implementation, parameterization, and validation of the all-atom continuous constant pH MD (CpHMD) method with particle-mesh Ewald (PME) electrostatics in the Amber22 pmemd. cuda engine. The titration parameters for Asp, Glu, His, Cys, and Lys were derived for the CHARMM c22 and Amber ff14sb and ff19sb force fields. We then evaluated the PME-CpHMD method using the asynchronous pH replica-exchange titration simulations with the c22 force field for six benchmark proteins, including BBL, hen egg white lysozyme (HEWL), staphylococcal nuclease (SNase), thioredoxin, ribonuclease A (RNaseA), and human muscle creatine kinase (HMCK). The root-mean-square deviation from the experimental pKas of Asp, Glu, His, and Cys is 0.76 pH units, and the Pearsons correlation coefficient for the pKa shifts with respect to model values is 0.80. We demonstrated that a finite-size correction or much enlarged simulation box size can remove a systematic error of the calculated pKas and improve agreement with experiment. Importantly, the simulations captured the relevant biology in several challenging cases, e.g., the titration order of the catalytic dyad Glu35/Asp52 in HEWL and the coupled residues Asp19/Asp21 in SNase, the large pKa upshift of the deeply buried catalytic Asp26 in thioredoxin, and the large pKa downshift of the deeply buried catalytic Cys283 in HMCK. We anticipate that PME-CpHMD offers proper pH control to improve the accuracies of MD simulations and enables mechanistic studies of proton-coupled dynamical processes that are ubiquitous in biology but remain poorly understood due to the lack of experimental tools and limitation of current MD simulations.

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Harris, J. A., Liu, R., Martins de Oliveira, V., Vazquez Montelongo, E., Henderson, J. A., Shen, J.. 2022-06-05. GPU-Accelerated All-atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber. https://doi.org/10.1101/2022.06.04.494833

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