Skip Navigation



Bioinformatics Advance Access published online on December 21, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti213
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/8/1603    most recent
bti213v2
bti213v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Hatzimanikatis, V.
Right arrow Articles by Broadbelt, L. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hatzimanikatis, V.
Right arrow Articles by Broadbelt, L. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics © Oxford University Press 2004; all rights reserved.
Received August 30, 2004
Revised November 16, 2004
Accepted December 8, 2004

Article

Exploring the diversity of complex metabolic networks

Vassily Hatzimanikatis 1*, Chunhui Li 1, Justin A. Ionita 1, Christopher S. Henry 1, Matthew D. Jankowski 1, and Linda J. Broadbelt 1

1 Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL

* To whom correspondence should be addressed.
Vassily Hatzimanikatis, E-mail: vassily{at}northwestern.edu


  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 we discovered almost 75,000 novel biochemical routes from chorismate to phenylalanine, more than 350,000 from chorismate to tyrosine, and 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).


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
M. J. L. de Groot, R. J. P. van Berlo, W. A. van Winden, P. J. T. Verheijen, M. J. T. Reinders, and D. de Ridder
Metabolite and reaction inference based on enzyme specificities
Bioinformatics, November 15, 2009; 25(22): 2975 - 2982.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. Rodrigo, J. Carrera, K. J. Prather, and A. Jaramillo
DESHARKY: automatic design of metabolic pathways for optimal cell growth
Bioinformatics, November 1, 2008; 24(21): 2554 - 2556.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Mu, P. J. Unkefer, C. J. Unkefer, and W. S. Hlavacek
Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites
Bioinformatics, December 15, 2006; 22(24): 3082 - 3088.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. L. Reed, T. R. Patel, K. H. Chen, A. R. Joyce, M. K. Applebee, C. D. Herring, O. T. Bui, E. M. Knight, S. S. Fong, and B. O. Palsson
Systems approach to refining genome annotation
PNAS, November 14, 2006; 103(46): 17480 - 17484.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.