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An enzyme mechanism language for the mathematical modeling of metabolic pathways

Chin-Rang Yang
Bruce E Shapiro
Organization: Caltech
Department: Control and Dynamical Systems
Eric Mjolsness
Organization: University of California, Irvine
Department: Department of Information and Computer Science
G. Wesley Hatfield
Journal / Anthology

Year: 2005
Volume: 21
Issue: 6
Page range: 774-780

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.

*Science > Biochemistry