Computational approaches to the display and manipulation of metabolic pathways : theory and practice

Abstract

Since metabolic pathways constitute a complex system, a mathematical description, even a structural one, must be simplified. Yet, the model must be sufficiently general so that it will encompass the system that is to be represented. An approach is presented for representing metabolic reaction systems. It uses simple object bipartite graphs, with event operators (mediators of events) representing one species and non-operators (the non-mediators in events) the other. Edge colours describe relations between the two species and shared objects connect events together. The operators (e.g., enzymes) are integral components of the system interacting with the non-operators (e.g., substrates). This facilitates inclusion of receptors and transporters (operators), and effectors (non-operators) in the same model. A membrane operator separates two compartments and mediates the transport of compounds between them. Furthermore, enclosing a sequence of events between two membrane operators represents compartmentalisation of that sequence. Extended operators can include additional information such as the species and chromosome. Non-enzymatic reactions are included in the model by treating the activation energy as the operator. An operator in one event may be a non-operator in another, and vice versa. This is useful for addressing conceptual issues such as representing an enzyme as substrate (e.g., phosphorylation) or a metabolite (e.g., cyclic AMP) as mediator in a signal transduction pathway.