Comparing Free Energy Diagrams of Enzyme-Catalyzed Reactions to Un-Catalyzed Reactions

다국어 초록 (Multilingual Abstract)

Generalized kinetics for comparing enzyme -catalyzed and un-catalyzed reaction kinetics within the traditional thermodynamic box examined with the aid of a new convention. If the concentration of substrate is set equal to its dissociation constants and the concentration of enzyme is adjusted so that rates of reaction are equal. then the catalytic power of the enzyme must be algebraically equal to the ratio of these two concentrations, or [S]/[E]. This singular, model-independent assessment avoids ambiguities associated with comparisons at the extremes of high and low concentration of substrate, and normalizes molecularities within and between reactions. Normalized free energy diagrams for differing mechanisms of enhancing rates of catalysis, such as stabilizing the transition-state or destabilizing the reactant ground-state, are identical which resolves recent and long term controversies and suggests that isolated changes in free energy diagrams without normalization may be misleading. The use of a diffusion-controlled Kcat/Km as a criterion for a perfectly evolved enzymes is challenged : (a) because diffusion-controlled kinetics may obtain also when the catalytic power is compromised, (b) because Kcat,/Km does not encompass a complete turmover and is insensitive to late partially rate-limiting steps, and (c) because rates of diffusion for different substrates and enzymes differ, which renders the endpoint of a comparison uncertain. As an altermative that is free of these limitations, a new criterion is offered: a Km which exceeds physiological concentrations of substrate by two-fold or more requires an enzyme to be operating physiologically within 50% of the diffusion-controlled limit.