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Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Applications Note

A general computational model of mitochondrial metabolism in a whole organelle scale

Katsuyuki Yugi and Masaru Tomita *

Institute for Advanced Biosciences, Keio University, Endo 5322, Fujisawa, Kanagawa, 252-8520, Japan

Received on September 16, 2003; revised on December 16, 2003; accepted on December 29, 2003
Advance Access Publication February 12, 2004

Summary: A computational tool for mitochondrial systems biology has been developed as a simulation model of E-Cell2, a publicly available simulation system. The general model consists of 58 enzymatic reactions and 117 metabolites, representing the respiratory chain, the TCA cycle, the fatty acid ß-oxidation and the inner-membrane transport system. It is based on previously published enzyme kinetics studies in the literature; we have successfully integrated and packaged them into a single large model. The model can be easily extended and modified so that mitochondrial biologists/physiologists can integrate their own models and evaluate them in the context of the whole organelle metabolism.

Availability: The mitochondrial model is bundled up with E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences.

Supplementary information: All the kinetic data are available via http://www.e-cell.org

Contact: chaos{at}e-cell.org

* To whom correspondence should be addressed.


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