Stoichiometric modelling of cell metabolism

There are several methodologies based on representations of cell metabolism that share two characteristics: the use of a metabolic network and the assumption of pseudosteady state. These methodologies have different purposes, employ different mathematical tools and are based on different assumptions; however, they all exploit the properties of a similar mathematical description. In this article we use the term stoichiometric modelling to encompass all these methodologies and to describe them within a common framework. Although the information about reaction stoichiometry embedded in metabolic networks is highly important, the framework encompasses methodologies not limited to the use of stoichiometric information. To highlight this fact, the definition of the framework is approached from a constraint-based perspective. One of the reasons for the success of stoichiometric modelling is that it avoids the difficulties that arise in the development of kinetic models: a consequence of the lack of intracellular experimental measurements. Thus, it makes it possible to exploit the knowledge about the structure of cell metabolism, without considering the still not very well known intracellular kinetic processes. Stoichiometric models have been used to estimate the metabolic flux distribution under given circumstances in the cell at some given moment (metabolic flux analysis), to predict it on the basis of some optimality hypothesis (flux balance analysis), and as tools for the structural analysis of metabolism providing information about systemic characteristics of the cell under investigation (network-based pathway analysis).