The structural factors responsible for the rapid rates (k(cat)s) of enzyme-catalyzed reactions are not well understood. In this paper, we outline an analysis that we believe can provide a quantitative understanding of the k(cat)s of three types of reactions: abstraction of the α-protons from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters. We propose that these reactions proceed via the formation of intermediates in which negative charge develops on the carbonyl or phosphoryl oxygens. Our analysis is based on Marcus formalism that separates the activation energy barrier for conversion of bound substrate to the intermediate, ΔG, into contributions from a thermodynamic barrier, ΔG(o), and an intrinsic kinetic barrier, ΔG(int). We propose that one (or more) general acid catalyst positioned adjacent to the carbonyl or phosphoryl oxygens of the substrate is primarily responsible for reducing both ΔG(o) and ΔG(int) from the values that characterize nonenzymatic reactions. The proton donors (1) stabilize the intermediates via the formation of short, strong hydrogen bonds (the pK(a)s of the protonated intermediates and the general acid catalysts are matched), thereby reducing ΔG(o), and (2) stabilize the transition states for formation of the intermediates by negating the developing charge on the oxygens without the requirement for significant structural reorganization, thereby reducing ΔG(int). The possible reductions in ΔG(o) and ΔG(int) are sufficient to understand the rapid k(cat)s of these reactions.
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