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ChloroKB ( http://chlorokb.fr ) is a knowledge base providing synoptic representations of the metabolism of the model plant Arabidopsis thaliana and its regulation. Initially focused on plastid metabolism, ChloroKB now accounts for the metabolism throughout the cell. ChloroKB is based on the CellDesigner formalism. CellDesigner supports graphical notation and listing of the corresponding symbols based on the Systems Biology Graphical Notation. Thus, this formalism allows biologists to represent detailed biochemical processes in a way that can be easily understood and shared, facilitating communication between researchers. In this chapter, we will focus on a specificity of ChloroKB, the representation of multilayered regulation of protein activity. Information on regulation of protein activity is indeed central to understanding the plant response to fluctuating environmental conditions. However, the intrinsic diversity of the regulatory modes and the abundance of detail may hamper comprehension of the regulatory processes described in ChloroKB. With this chapter, ChloroKB users will be guided through the representation of these sophisticated biological processes of prime importance to understanding metabolism or for applied purposes. The descriptions provided, which summarize years of work and a broad bibliography in a few pages, can help speed up the integration of regulatory processes in kinetic models of plant metabolism., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

This chapter describes a practical procedure to dissect metabolic systems, simplify them, and use or derive enzyme rate equations in order to build a mathematical model of a metabolic system and run simulations. We first deal with a simple example, modeling a single enzyme that follows Michaelis-Menten kinetics and operates in the middle of an unbranched metabolic pathway. Next we describe the rules that can be followed to isolate sub-systems from their environment to simulate their behavior. Finally we use examples to show how to derive suitable rate equations, simpler than those needed for mechanistic studies, though adequate to describe the behavior over the physiological range of conditions.Many of the general characteristics of kinetic models will be obvious to readers familiar with the theory of metabolic control analysis (Cornish-Bowden, Fundamentals of Enzyme Kinetics, Wiley-Blackwell, Weinheim, 327-380, 2012), but here we shall not assume such knowledge, as the chapter is directed toward practical application rather than theory.