Exploring the diversity of complex metabolic networks

Vassily Hatzimanikatis*, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

229 Scopus citations

Abstract

Motivation: Metabolism, the network of chemical 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 biochemical 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 thermodynamic properties. Results: We applied this framework to the analysis of the aromatic amino acid pathways and discovered almost 75 000 novel biochemical routes from chorismate to phenylalanine, more than 350 000 from chorismate to tyrosine, but only 13 from chorismate to tryptophan. Thermodynamic analysis of these pathways suggests that the native pathways are thermodynamically more favorable than the alternative possible pathways. The pathways generated involve compounds that exist in biological databases, as well as compounds that exist in chemical databases and novel compounds, suggesting novel biochemical routes for these compounds and the existence of biochemical compounds that remain to be discovered or synthesized through enzyme and pathway engineering.

Original languageEnglish (US)
Pages (from-to)1603-1609
Number of pages7
JournalBioinformatics
Volume21
Issue number8
DOIs
StatePublished - Apr 15 2005

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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