Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.

Buried charged residues play important roles in the modulation of protein stabilities and conformational dynamics and make crucial contributions to protein functions. Considering the generally nonpolar nature of protein interior, a key question concerns the contribution of electronic polarization to the stabilization and properties of buried charges. We answer this question by conducting free energy simulations using the latest polarizable CHARMM force field based on Drude oscillators for a series of nuclease mutants that involve a buried Glu-Lys pair in different titration states and orientations. While a nonpolarizable model suggests that the ionized form of the buried Glu-Lys pair is more than 40 kcal/mol less stable than the charge-neutral form, the two titration states are comparable in stability when electronic polarization is included explicitly, a result better reconcilable with available experimental data. Analysis of free energy components suggests that additional stabilization of the ionized Glu-Lys pair has contributions from both the enhanced salt-bridge strength and stronger interaction between the ion-pair and surrounding protein residues and penetrated water. Despite the stronger direct interaction between Glu and Lys, the ion-pair exhibits considerably larger and faster structural fluctuations when polarization is included, due to compensation of interactions in the cavity. Collectively, observations from this work provide compelling evidence that electronic polarization is essential to the stability, hydration, dynamics, and therefore function of buried charges in proteins. Therefore, our study advocates for the explicit consideration of electronic polarization for mechanistic and engineering studies that implicate buried charged residues, such as enzymes and ion transporters.