An enzyme mechanism language for the mathematical modeling of metabolic pathways

Authors:
Chin-Rang Yang;Bruce E. Shapiro;Eric D. Mjolsness;G. Wesley Hatfield
Affiliations:
Department of Microbiology and Molecular Genetics, College of Medicine, University of California Irvine, CA 92697, USA;Jet Propulsion Laboratory, California Institute of Technology 4800 Oak Grove Drive, Pasadena, CA 91109, USA;School of Information and Computer Science, University of California Irvine, CA 92697, USA;Department of Microbiology and Molecular Genetics, College of Medicine, University of California Irvine, CA 92697, USA
Venue:
Bioinformatics
Year:
2005

Citing 0
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Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes

CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference

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Abstract

Motivation: As a first step toward the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways. Results: We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association--dissociation reactions that are translated by Cellerator into ordinary differential equations that are numerically solved by Mathematica™. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations. Availability: A Mathematica™ executable kMech.m file is available at the University of California, Irvine, Institute for Genomics and Bioinformatics website, http://www.igb.uci.edu/servers/sb.html. Cellerator, free of charge to academic, US government, and other non-profit organizations, can be obtained at the Cellerator website, (http://www-aig.jpl.nasa.gov/public/mls/cellerator/feedback.html). Contact: Biology correspondence should be addressed to gwhatfie@uci.edu. Computation correspondence should be addressed to emj@uci.edu. Supplementary information:http://www.igb.uci.edu/servers/sb.html.