Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism

Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism

Indexed in: EBSCO.

An understanding of biological systems at cellular and molecular levels helps researchers to model cellular behavior in different experimental conditions. This, in turn, can lead to insights about ...
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Kinetic Modeling for the Main Metabolic Pathways

Pp. 133-186 (54)

Kazuyuki Shimizu and Yu Matsuoka

Abstract

Kinetic models for the main metabolic pathways such as glycolysis, TCA cycle, pentose phosphate pathway together with anaplerotic pathways and gluconeogenic pathways are explained. Kinetic models for substrate uptake pathways such as glucose PTS, glycerol uptake pathways, and xylose assimilating pathways are then explained. Kinetic models for the fermentation pathways under anaerobic condition are also explained. Moreover, kinetic models for amino acid synthetic pathways such as glutamic acid/ glutamine synthetic pathways and lysine synthetic pathways are explained. Unlike flux balance analysis based on the stoichiometric constraints, kinetic modeling approach based on enzymatic reactions for the metabolic pathways can be easily extended for the inclusion of enzyme level and transcriptional regulations, and the kinetic models can reasonably express the dynamics.

Keywords:

Kinetic modeling, Embden-Meyerhoff-Parnas pathway, glycolysis, pentose phosphate pathway, TCA cycle, gluconeogenic pathway, amino acid synthesis, carbohydrate metabolism, nitrogen metabolism, anaerobic fermentation, lysine synthetic pathway.

Affiliation:

Institute of Advanced Biosciences Keio University Tsuruoka Yamagata 997-0017 Japan.