A Poisson-Boltzmann study of charge insertion in an enzyme active site: The effect of dielectric relaxation

Continuum solvent models are playing an increasing role in the study of aqu eous solutions, particularly those involving protein solutes. To estimate t he magnitude of dielectric relaxation and clarify the microscopic meaning o f the protein dielectric constant, charge insertion in the active site of t he enzyme aspartyl-tRNA synthetase (AspRS) is analyzed using finite-differe nce Poisson-Boltzmann calculations. The insertion process is a simplified m odel that mimics qualitatively the mutation of substrate Asp into Asn, stud ied earlier by free; energy simulations. A two-step insertion path gives th e relaxation and nonrelaxation ("static") free energy components separately . The assumption of linear response leads to a linear relation between the two components, connecting the explicit structural differences between reac tant and product structures with the relaxation free energy calculated from either structure. This relation is verified here only if protein dielectri c constants of 1 and 4-8 are used for the static and relaxation free energi es, respectively. These are also the only conditions that give reasonable a greement with the Asp --> Asn free energy simulated earlier and with a mole cular dynamics/linear response estimate of the present charging free energy . The use of two protein dielectric constants represents a significant depa rture from standard continuum models. The values obtained are physically re asonable: a protein dielectric of 4-8 for relaxation indicates that the act ive site of AspRS, though highly polar, is only moderately polarizable. A d ielectric of one for the static term indicates that the charge set, optimiz ed for explicit solvent simulations, reproduces the equilibrium potential w ithout the need for additional, implicit protein polarization. In contrast to simple charge insertion, the binding free energies of Asp and Asn to Asp RS are best calculated with a more standard protocol that uses a single pro tein dielectric of 4, accurately reproducing free energy simulation results . For this and other binding processes, additional fi ee energy components are involved, related to desolvation of the binding site; the optimal diele ctric constant represents an empirical compromise among these. A multistep component analysis could also be used to analyze the role of relaxation in these more complex processes. It is suggested that the use of more than one dielectric constant in continuum models will lead to a more consistent and robust description of dielectric phenomena in solution.