Mechanistic Model Development for Multi-Enzymatic Reactions in Lignin Biosynthesi

Modeling an enzymatic reaction, one unit of biomass regulation, enables a more comprehensive analysis of biosynthesis. Such modeling enables one to control each reaction rate for the product and, by extension, to use transgenic perturbation strategies. Modeling approaches have traditionally been confined to reactions catalyzed by a single enzyme. Reactions controlled by multiple enzymes, however, comprise a large proportion of various biosynthesis pathways such as lignin. Modeling a multi-enzymatic reaction presents a challenge due to unknown enzymeenzyme or enzyme-substrate interactions. New modeling approaches are needed to predict unknown interactions among components in multi-enzymatic reactions and to provide appropriate mathematical expressions.;The research in this dissertation presents two modeling approaches which develop mechanistic models for multi-enzymatic reactions. The first is for mechanistic models characterized by detailed inner components and interactions. This approach optimizes the model through analysis and assumptions based on mass action. It also develops the model structures and mathematical equations for multi-enzymatic reactions and provides reproduction and prediction of experimental reaction rates. The second provides simplified mechanistic models representing key relationships among the enzymes associated with the reaction rate. This approach is carried out through computational methodologies, a rule-based algorithm and an evolutionary computation algorithm, which contribute to a general insight about the mechanism of multi-enzyme reactions and also save model development time. This approach can be used as a tool which facilitates control of the early stages of a detailed mechanistic modeling.;These approaches were applied to multi-enzymatic reactions with different characteristics. These are important reactions to shape the final products in lignin biosynthesis. Biological relevance of the modeling results of these applications was assured by comparing them with previous literature and with the results of diverse experiment technologies. These tools will provide helpful insights in many research areas based on the functions of enzyme-regulated biochemical reactions.