Gerlt J A, Gassman P G
Department of Chemistry and Biochemistry, University of Maryland, College Park 20742.
Biochemistry. 1993 Nov 16;32(45):11943-52. doi: 10.1021/bi00096a001.
The structural factors responsible for the rapid rates (kcats) 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 kcats of three types of reactions: abstraction of the alpha-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, delta G++, into contributions from a thermodynamic barrier, delta G zero, and an intrinsic kinetic barrier, delta G++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 delta G zero and delta G++int from the values that characterize nonenzymatic reactions. The proton donors (1) stabilize the intermediates via the formation of short, strong hydrogen bonds (the pKas of the protonated intermediates and the general acid catalysts are matched), thereby reducing delta G zero, 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 delta G++int. The possible reductions in delta G zero and delta G++int are sufficient to understand the rapid kcats of these reactions.
目前对于酶催化反应快速速率（kcats）背后的结构因素尚未完全理解。在本文中，我们概述了一种分析方法，我们认为该方法能够对三类反应的kcats进行定量理解：从碳酸中提取α-质子的反应、酰基转移反应以及磷酸二酯的取代反应。我们提出这些反应通过形成中间体进行，在中间体中羰基或磷酰氧上会产生负电荷。我们的分析基于Marcus形式理论，该理论将结合底物转化为中间体的活化能垒（ΔG++）分为热力学垒（ΔG0）和本征动力学垒（ΔG++int）的贡献。我们提出，位于底物羰基或磷酰氧附近的一个（或多个）广义酸催化剂主要负责将非酶促反应特征值下的ΔG0和ΔG++int均降低。质子供体（1）通过形成短而强的氢键（质子化中间体和广义酸催化剂的pKa相匹配）来稳定中间体，从而降低ΔG0；（2）通过消除氧上产生的电荷而无需显著的结构重排来稳定中间体形成的过渡态，从而降低ΔG++int。ΔG0和ΔG++int的可能降低足以解释这些反应的快速kcats。
