Force Field Limitations\nof All-Atom Continuous Constant\npH Molecular Dynamics

All-atom constant pH molecular dynamics simulations offer\na powerful\ntool for understanding pH-mediated and proton-coupled biological processes.\nAs the protonation equilibria of protein side chains are shifted by\nelectrostatic interactions and desolvation energies, p<i>K</i><sub>a</sub> values calculated from the constant pH simulations may\nbe sensitive to the underlying protein force field and water model.\nHere we investigated the force field dependence of the all-atom particle\nmesh Ewald (PME) continuous constant pH (PME-CpHMD) simulations of\na mini-protein BBL. The replica-exchange titration simulations based\non the Amber ff19sb and ff14sb force fields with the respective water\nmodels showed significantly overestimated p<i>K</i><sub>a</sub> downshifts for a buried histidine (His166) and for two glutamic\nacids (Glu141 and Glu161) that are involved in salt-bridge interactions.\nThese errors (due to undersolvation of neutral histidines and overstabilization\nof salt bridges) are consistent with the previously reported p<i>K</i><sub>a</sub>’s based on the CHARMM c22/CMAP force\nfield, albeit in larger magnitudes. The p<i>K</i><sub>a</sub> calculations also demonstrated that ff19sb with OPC water is significantly\nmore accurate than ff14sb with TIP3P water, and the salt-bridge related\np<i>K</i><sub>a</sub> downshifts can be partially alleviated\nby the atom-pair specific Lennard-Jones corrections (NBFIX). Together,\nthese data suggest that the accuracies of the protonation equilibria\nof proteins from constant pH simulations can significantly benefit\nfrom improvements of force fields.