Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model

Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transf er reactions. Its complexity makes experimental characterization difficult, and so, theoretical approaches are valuable. The comparison of molecular d ynamics free. energy simulations with simpler models such as a dielectric c ontinuum model is especially useful for obtaining qualitative insights. We have analyzed a charge insertion process that models deprotonation or mutat ion of an important side chain in the active site of the enzyme aspartyl-tR NA synthetase. Complexes with the substrate aspartate and the analogue aspa ragine were studied. The resulting dielectric relaxation was found to invol ve both ligand and side chain rearrangements in the active site and to acco unt for a large part of the overall charging free energy. With the continuu m model, charge insertion is performed along a two-step pathway: insertion into a static environment, followed by relaxation of the environment. These correspond to different physical processes and require different protein d ielectric constants. A low value of similar to1 is needed for the static st ep, consistent with the parametrization of the molecular mechanics charge. set used. A value of 3-6 (depending on the exact insertion site and the nat ure of the ligand) is needed to describe the dielectric relaxation step. Th is moderate value indicates that, for this system, the local protein polari zability in the active site is within at most a factor of 2 of that expecte d at nonspecific positions in a protein interior.