Automatic Assembly and Calibration of Models of Enzymatic Reactions Based on Ordinary Differential Equations

Abstract

Enzymatic reactions have been studied for more than a 100 years. Indeed, isolation of enzymes from biological materials is no longer the main source of enzymes today, as they are now largely produced using recombinant technology, or can even be synthesized from scratch. Studies of the three-dimensional structures of enzymes can provide answers to many questions, but the kinetics of enzymatic reactions is the only method that can lead to better understanding of their function. The complexity of high-throughput analysis of progress curves of data obtained can only be achieved through numerical solutions of a suitable system of ordinary differential equations. We have developed the freely available server ENZO: a web tool for derivation and evaluation of kinetic models of enzyme-catalyzed reactions ( http://enzo.cmm.ki.si/ ). ENZO can be used for simultaneous analysis of a series of progress curves obtained under many different conditions. In this chapter, we exemplify the principles and possibilities of this type of high-throughput analysis.

Keywords: ENZO; Enzyme-catalyzed reactions; Kinetic models; Ordinary differential equations.