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

Abstract

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 Staphylococcal 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.

Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA

“…The physical properties and behaviors of water in the enzyme active sites can be distinct from those in the bulk and may make unique contributions to catalytic efficiency. ,− It is often argued that a low level of active site hydration is desired for efficient catalysis due to lower reorganization energy relative to bulk solution. ,, However, both AP and PafA are highly efficient enzymes despite their solvent-accessible active sites. Our analysis of PafA variants clearly indicates that the hydration level of the active site can be tuned by second-shell mutations (e.g., A302V and D163V) through a combination of steric effects that modulate the active site volume and modification of local hydrophobicity (Figures g and S8).…”

“…Our analysis of PafA and related enzymes , suggests that explicitly predicting and optimizing active site hydration level and water-mediated hydrogen-bonding networks using efficient computational tools − should be an integral part of rational enzyme design. Indeed, by controlling the hydration level of the active site and dielectric properties of these confined waters, , it is possible to take advantage of the nonadditivity of hydrogen-bonding interactions, which enables second-shell residues to polarize first-shell residues and enhance the stabilization of reactive moieties. For instance, one strategy is to place divalent metal ions such as Mg 2+ to modulate active site reactivities through electrostatics and/or metal–ligand-mediated interactions.…”

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

“…The development of protein polarizable force fields has advanced significantly in the past decade, − in particular, the AMOEBA force field based on point-induced dipole , and the Drude force field based on classical Drude oscillator. − Polarizable force fields have been used to reveal the importance of polarization effects in modeling salt bridge interactions in proteins, ion binding and selectivity, , helix formation, amyloid aggregation, and protein–ligand binding processes. − The recently developed Drude-2019 protein force field has further enhanced the accuracy of protein dynamics through adjustments of the polarizabilities of select C atoms, reoptimized of side chain χ 1 , χ 2 dihedral parameters, and improved description of the interactions between charged residues . To the best of our knowledge, the Drude polarizable force fields have not been applied to study peptide nanotube systems.…”

Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent

“…Furthermore, an RESP method has been proposed to make the ESP-derived charges more suitable for molecular dynamics (MD) simulations . The RESP charges, derived from gas-phase HF/6-31G* calculations, have been extensively utilized in the development of force fields for modeling proteins, DNAs, RNAs, and drug-like molecules in MD simulations. ,,,− ,,− However, studies have suggested that the ESP-based electrostatic parameters should vary to accurately describe EIs in response to changes in the polarity of the environment. , Accordingly, many advanced polarizable force fields were developed for improving accuracy of the force fields in tackling the EIs. − Nonetheless, compared to fixed charge force fields, polarizable force fields require additional computational cost to accurately capture polarization energy. This increased computational overhead reduces their efficiency and limits their widespread use in MD simulations.…”