Exploring the diversity of complex metabolic networks

Motivation: Metab., the network of chem. reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochem. reaction from a given set of enzyme reaction rules that allows the de novo synthesis of metabolic pathways composed of these reactions, and the evaluation of these novel pathways with respect to their thermodn. properties. Results: We applied this framework to the anal. of the arom. amino acid pathways and discovered almost 75,000 novel biochem. routes from chorismate to phenylalanine, more than 350,000 from chorismate to tyrosine, but only 13 from chorismate to tryptophan. Thermodn. anal. of these pathways suggests that the native pathways are thermodynamically more favorable than the alternative possible pathways. The pathways generated involve compds. that exist in biol. databases, as well as compds. that exist in chem. databases and novel compds., suggesting novel biochem. routes for these compds. and the existence of biochem. compds. that remain to be discovered or synthesized through enzyme and pathway engineering. [on SciFinder (R)