THE DETERMINANTS OF PK(A)S IN PROTEINS

Although validation studies show that theoretical models for predictin g the pK(a)s of ionizable groups in proteins are increasingly accurate , a number of important questions remain: (1) What factors limit the a ccuracy of current models? (2) How can conformational flexibility of p roteins best be accounted for? (3) Will use of solution structures in the calculations, rather than crystal structures, improve the accuracy of the computed pK(a)s? and (4) Why does accurate prediction of prote in pK(a)s seem to require that a high dielectric constant be assigned to the protein interior? This paper addresses these and related issues . Among the conclusions are the following: (1) computed pK(a)s average d over NMR structure sets are more accurate than those based upon sing le crystal structures; (2) use of atomic parameters optimized to repro duce hydration energies of small molecules improves agreement with exp eriment when a low protein dielectric constant is assumed; (3) despite use of NMR structures and optimized atomic parameters, pK(a)s compute d with a protein dielectric constant of 20 are more accurate than thos e computed with a low protein dielectric constant; (4) the pK(a) shift s in ribonuclease A that result from phosphate binding are reproduced reasonably well by calculations; (5) the substantial pK(a) shifts obse rved in turkey ovomucoid third domain result largely from interactions among ionized groups; and (6) both experimental data and calculations indicate that proteins tend to lower the pK(a)s of Asp side chains bu t have little overall effect upon the pK(a)s of other ionizable groups .