Title: "An Enzyme Mechanism Language for the Mathematical Modeling of Metabolic Pathways"
Speaker: Dr. Chin-Rang Yang
Place: SMITH 108; Tuesday, 4:30pm


Motivation: As a first step towards the elucidation of the systems biology of the model organism, Escherichia coli, it was our goal to mathematically model a metabolic system of intermediate complexity, the well-studied end-product regulated pathways for the biosynthesis of the branched chain amino acids, L-isoleucine, L-valine, and L-leucine.

Results: In this report we describe kMech. a Cellerator language extension that describes a suite of eleven enzyme mechanisms suitable for the mathematical modeling of the branched chain amino acid biosynthetic pathways of E. coli. Each enzyme mechanism of this model is parsed by kMech into a set of fundamental association-dissociation reactions that are translated by Cellerator into ordinary differential equations (ODEs) that are numerically solved by MathematicaTM. We present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations. We demonstrate that simulations of metabolic and genetic perturbations of this model predict experimentally observed results.

Availability: A MathematicaTM executable, kMech.m, file and a MathamaticaTM notebook file for the simulation of branched chain amino acid biosynthesis, may be downloaded from the University of California, Irvine, Institute for Genomics and Bioinformatics website at www.igb.uci.edu/tools.htm.

Supplementary Information: http://www.igb.uci.edu/servers/coli/coli.htm.

(This is a candidate for the Bioinformatics COALESCE hires in the School of Science. To meet with the candidate, please contact RW Doerge at doerge@purdue.edu)

See http://www.stat.purdue.edu/~doerge/BIOINFORM.D/SPRING04/sem.html for a full scheule of BIOINFORMATICS SEMINARS.