Exploring the diversity of complex metabolic networks

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...

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Bibliographic Details
Published in:Bioinformatics 2005-04, Vol.21 (8), p.1603-1609
Main Authors: Hatzimanikatis, Vassily, Li, Chunhui, Ionita, Justin A., Henry, Christopher S., Jankowski, Matthew D., Broadbelt, Linda J.
Format: Article
Language:English
Subjects:
Amino Acids, Aromatic - metabolism
Animals
Biodiversity
Biological and medical sciences
Computer Graphics
Computer Simulation
Energy Metabolism - physiology
Feasibility Studies
Fundamental and applied biological sciences. Psychology
General aspects
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Biological
Models, Chemical
Multienzyme Complexes - metabolism
Signal Transduction - physiology
User-Computer Interface
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Summary: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. Availability: Framework will be available via web interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). Contact: vassily@northwestern.edu or broadbelt@northwestern.edu Supplementary information: http://systemsbiology.northwestern.edu/BNICE/publications
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti213