Electrostatic effects in proteins are governed by pH-redistribution of the conformational ensemble

The imperative for charges to be hydrated is one of the most important organizing principles in biology, responsible for the general architecture of biological macromolecules and for energy storage in the form of electrochemical gradients. Paradoxically, many functional sites in proteins have buried ionizable groups. These groups are tolerated because they are usually buried in the neutral state. However, when they become charged they can drive structural transitions to open states in which the charge can be stabilized, mostly through interactions with water. This coupling between the ionization of a buried group and conformational reorganization is precisely the mechanism used by proteins to perform energy transduction. By applying this principle to a family of 25 variants of staphylococcal nuclease with internal Lys residues, it was possible to characterize in detail the range of localized partial unfolding events that even a highly stable protein that unfolds cooperatively can undergo in response to H+-binding. Conformational states that constitute vanishingly small populations of the equilibrium native state ensemble of this protein were identified by correlation of structural and thermodynamic data, providing a map of the conformational landscape of this protein with unprecedented detail. The data demonstrate that the apparent pKa values of buried ionizable residues are not determined by the properties of their microenvironment but by the intrinsic propensity of the protein to populate open states in which internal charged residues can be hydrated. The role of buried residues in functional sites in proteins relies on their ability to tune the conformational ensemble for redistribution in response to small changes in pH. These results provide the physical framework necessary for understanding the role of pH-driven conformational changes in driving biological energy transduction, the identification of pH-sensing proteins in nature, and for the engineering of pH-sensitive dynamics and function in de novo designed proteins.