p Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model.

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Titlep Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model.
Publication TypeJournal Article
Year of Publication2020
AuthorsAleksandrov, A, Roux, B, Mackerell, AD
JournalJ Chem Theory Comput
Date Published2020 Jun 12
ISSN1549-9626
Abstract

Electronic polarization effects have been suggested to play an important role in proton binding to titratable residues in proteins. In this work, we describe a new computational method for p calculations, using Monte Carlo (MC) simulations to sample protein protonation states with the Drude polarizable force field and Poisson-Boltzmann (PB) continuum electrostatic solvent model. While the most populated protonation states at the selected pH, corresponding to residues that are half-protonated at that pH, are sampled using the exact relative free energies computed with Drude particles optimized in the field of the PB implicit solvation model, we introduce an approximation for the protein polarization of low-populated protonation states to reduce the computational cost. The highly populated protonation states used to compute the polarization and p's are then iteratively improved until convergence. It is shown that for lysozyme, when considering 9 of the 18 titratable residues, the new method converged within two iterations with computed p's differing only by 0.02 pH units from p's estimated with the exact approach. Application of the method to predict p's of 94 titratable side chains in 8 proteins shows the Drude-PB model to produce physically more correct results as compared to the additive CHARMM36 (C36) force field (FF). With a dielectric constant of two assigned to the protein interior the Root Mean Square (RMS) deviation between computed and experimental p's is 2.07 and 3.19 pH units with the Drude and C36 models, respectively, and the RMS deviation using the Drude-PB model is relatively insensitive to the choice of the internal dielectric constant in contrast to the additive C36 model. At the higher internal dielectric constant of 20, p's computed with the additive C36 model converge to the results obtained with the Drude polarizable force field, indicating the need to artificially overestimate electrostatic screening in a nonphysical way with the additive FF. In addition, inclusion of both and orientations of the proton in the neutral state of acidic groups is shown to yield improved agreement with experiment. The present work, which is the first example of the use of a polarizable model for the prediction of p's in proteins, shows that the use of a polarizable model represents a more physically correct model for the treatment of electrostatic contributions to p shifts in proteins.

DOI10.1021/acs.jctc.0c00111
Alternate JournalJ Chem Theory Comput
PubMed ID32464053