Computer simulation of Escherichia coli metabolic pathways based on matabolome data

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1. We constructed a computer model of the Escherichia coli metabolic pathways using E-CELL simulation system. The model contained 190 enzymatic reactions that are responsible for central metabolic pathways such as glycolysis, the TCA cycle, the pentose phosphate pathway and the nucleotide biosynthesis pathways.2. For constructing this model, we initially developed a detection method for whole metabolites in E. coli by using capillary electrophoresis mass spectrometry (CE-MS) system. This method was applied to the comprehensive analysis of metabolic intermediates extracted from E. coli, hundreds of metabolites could be detected for collecting parameters in computer simulation.3. We developed a computational technique to assist in the large-scale identification of charged metabolites. The electrophoretic mobility of metabolites in CE-MS was predicted from their structure, using an ensemble of artificial neural networks (ANNs).4. We also developed a synthetic in vitro glycolysis system using ten purified E. coli enzymes to obtain kinetics for the computer simulation.