IMPROVING THE CONTINUUM DIELECTRIC APPROACH TO CALCULATING PK(A)S OF IONIZABLE GROUPS IN PROTEINS

The pH-dependent characteristics of a protein are determined by the pK (a)s of its titratable residues, Continuum electrostatic approaches pr ovide a fast means of calculating the pK(a)s of the titratable residue s in proteins immersed in aqueous ionic solution. Here, we show how op timization of the parameters used in continuum electrostatic calculati ons can lead to significant improvements in the accuracy of pK(a) pred ictions. Dependence on the protein dielectric constant is studied, and two classes of ionizable sites are identified: (1) a large number of mostly solvent exposed residues for which the best pK(a) is calculated if the protein dielectric constant is set close to that of the aqueou s solvent; and (2) a small number of mostly buried residues for which the best pK(a) is calculated with a lower site-specific protein dielec tric constant, These two classes of ionizable sites can be distinguish ed using a criterion based on desolvation energy, A priori determinati on of the optimum protein dielectric constant for the second class is not easy, but satisfactory results are obtained if it is assigned in t he range 10-20, The accuracy of the calculated pK(a)s is influenced by the assignment of proton positions and we suggest modifications to th e OPLS parameter set that eliminate the need to construct hypothetical , and therefore error prone, proton positions during the calculation p rocedure, For the test set of proteins studied, the final recommended protocol enables the tautomers of histidine residues to be assigned au tomatically, the pK(a)s of residues in the ''high dielectric constant' ' class to be calculated to within 0.7 pK(a) units, and the pK(a)s of residues in the ''low dielectric constant'' class to be calculated to within 1.6 pK(a) units.