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

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 pK_a 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. Th

SUBMITTER: Aleksandrov A 

PROVIDER: S-EPMC7428141 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature