Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark

One of the most useful ways of describing and analyzing enzyme catalysis is the description of the enzyme as an effective solvent for the reacting substrate. Here, we illustrate this concept by considering the S(N)2 reaction of haloalkan dehalogenase (DhlA), analyze the energetics and dynamics of the solvent coordinate, and evaluate their relative catalytic effect. It is demonstrated that almost the entire catalytic effect is associated with the preorganization of the protein-solvent coordinate. It is clarified that this effect is associated with the fact that the transition state is "solvated" by the protein more than in the reference solution reaction. This effect is fundamentally different than the frequently proposed desolvation mechanism. The possible catalytic role of dynamical effects is analyzed by considering several reasonable ways of defining "dynamical contributions to catalysis". It is found that these contributions are small regardless of the definition used. It is also shown that the effect of the difference in the relaxation time of the solvent coordinate in the enzyme and solution reaction is rather trivial relative to the effect of the corresponding changes in reorganization free energy.