Conformational Relaxation and Water Penetration Triggered by the Ionization of Internal Groups in Proteins

Abstract

Internal ionizable groups in proteins play essential functional roles in biochemical processes related to bioenergetics, including catalysis, proton transport, and electron transfer reactions. Many proteins harness the coupling between the ionization of internal groups and structural reorganization for functional purposes. To elucidate the mechanisms and the structural basis of function in these proteins, it is necessary to understand how the ionization of internal groups is coupled to structural reorganization of the protein and how the protein environment influences the pKa values of internal groups. Through molecular dynamics simulations and Self-guided Langevin dynamics simulations we are studying the types of structural responses that can be triggered by ionization of internal groups. Water penetration, side-chain rotation and backbone relaxation are among the structural changes that have been detected with molecular dynamics simulations. A large family of variants of staphylococcal nuclease with internal ionizable groups (Lys, Arg, Asp and Glu) are being used to examine these issues systematically. Some of the ionizable groups exhibit pKa values that are shifted significantly compared to the normal values in bulk water. Most computational methods for pKa calculations cannot reproduce accurately the pKa shifts observed in such variants, primarily because they cannot reproduce correctly the structural response to the ionization of internal groups. The physical and structural insight into structural changes promoted by internal charges will be useful to guide the development of more accurate methods for structure-based pKa calculations.