Proton binding to proteins: A free-energy component analysis using a dielectric continuum model

Proton binding plays a critical role in protein structure and function. We report pK_a calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. Averaging over conformations from the two endpoints of the proton-binding reaction, the protein's atomic degrees of freedom are explicitly modeled. Treating macroscopically the protein's electronic polarizability and the solvent, a meaningful model is obtained, without adjustable parameters. It reproduces qualitatively the electrostatic potentials, proton-binding free energies, Marcus reorganization free energies, and pK_a shifts from explicit solvent molecular dynamics simulations, and the pK_a shifts from experiment. For thioredoxin Asp-26, which has a large pK_a upshift, we correctly capture the balance between unfavorable carboxylate desolvation and favorable interactions with a nearby lysine; similarly for RNase A Asp-14, which has a large pK_a downshift. For the unshifted thioredoxin Asp-20, desolvation by the protein cavity is overestimated by 2.9 pK_a units; several effects could explain this. "Standard" Poisson-Boltzmann methods sidestep this problem by using a large, ad hoc protein dielectric; but protein charge-charge interactions are then incorrectly downscaled, giving an unbalanced description of the reaction and a large error for the shifted pK_a values of Asp-26 and Asp-14.