The Determinants of Carboxyl pKa Values in Turkey Ovomucoid Third Domain

A computational methodology for protein pKa predictions, based on ab initio quantum mechanical treatment of part of the protein and linear Poisson–Boltzmann equation treatment of the bulk solvent, is presented. The method is used to predict and interpret the pKa values of the five carboxyl residues (Asp7, Glu10, Glu19, Asp27, and Glu43) in the serine protease inhibitor turkey ovomucoid third domain. All the predicted pKa values are within 0.5 pH units of experiment, with a root-mean-square deviation of 0.31 pH units. We show that the decreased pKa values observed for some of the residues are primarily due to hydrogen bonds to the carboxyl oxygens. Hydrogen bonds involving amide protons are shown to be particularly important, and the effect of hydrogen bonding is shown to be nonadditive. Hydrophobic effects are also shown to be important in raising the pKa. Interactions with charged residues are shown to have relatively little effect on the carboxyl pKa values in this protein, in general agreement with experiment. Proteins 2004;55:000–000. © 2004 Wiley-Liss, Inc.