Transient-state kinetics and computational analysis of transcription initiation

Abstract

Abstract Transient-state kinetics is an important area of research to investigate the pathway of enzymatic reactions (1-6). Specific experiments are designed to follow the formation and decay of reacting species as a function of time. The concentrations are determined either directly by radiometric methods or indirectly through optical changes associated with the formation of intermediates and products. The kinetics is measured as a function of a second variable such as concentration of enzyme or substrate, based on which a model or a kinetic pathway is constructed. The kinetic data in most cases are too complex and hence best analysed by computational methods that make no assumptions in fitting the data, except for the model chosen by the investigator (7, 8). Several types of experiments including kinetic and equilibrium types are globally fit using numerical and least squares fitting methods to derive a set of intrinsic rate constants that reveals the pathway of the enzymatic reaction. The derived model is considered a working model that makes predictions, based on which new experiments are designed. The results of these experiments are used to refine the model.