Chemical Organisations in the Central Sugar Metabolism of Escherichia Coli

Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich (2006)
Chemical organizations in the central sugar metabolism of Escherichia Coli
In: Modeling and Simulation in Science Engineering and Technology, Post-proceedings of ECMTB 2005 
preprint (pdf)


The theory of chemical organisations is employed as a novel method to analyse and understand biological network models. The method allows to decompose a chemical reaction network into sub-networks that are (algebraically) closed and self-maintaining. Such sub-networks are termed organisations. Although only stoichiometry is considered to compute organisations, the analysis allows to narrow down the potential dynamic behaviour of the network: organisations represent potential steady state compositions of the system. When applied to a model of sugar metabolism in E. coli including gene expression, signal transduction, and enzymatic activities, some organisations are found to coincide with inducible biochemical pathways.