18] Compartmental analysis of enzyme-catalyzed reactions

Abstract

This chapter discusses the compartmental analysis of the chemistry of enzyme catalyzed reactions. It presents a background to the development and evolution of chemistry of enzyme catalyzed reactions. The chapter illustrates an example in which the analysis of the time-resolved kinetics of a restriction endonuclease-catalyzed reaction is accomplished by compartmental analysis using methodology developed by Berman and colleagues. Traditionally, in the analysis of complex kinetic data, a model is proposed and the corresponding differential equations are written and solved numerically. This sequence must be repeated for succeeding models. The process is tedious, computationally intensive, and, therefore, not often employed except for simple systems. High turnover and low substrate affinity are the signatures of the enzymes of intermediary metabolism. In the analysis of enzyme kinetics by the steady-state approach, it is the differential (rate) equation that is directly analyzed. With the approach of Berman, the kinetic data are analyzed first to determine the relations between compartments using an interactive program for model simulation and data analysis. Subsequently, the compartmental model is interpreted in terms of chemical processes. These processes are represented as transfers of species from one compartment to another. A compartment may be a unique chemical species, or it may be several chemical species. The program SAAM/CONSAM, an interactive program for simulation, analysis, and modeling, has the advantage that models may be easily developed and modified. The chapter presents an application of this type of kinetic analysis to a restriction endonuclease using Bam HI as a model system and shows that the cleavage process may be easily resolved into separate binding and hydrolytic steps.