Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.

ABSTRACT:

Background

Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes.

Results

We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints.

SUBMITTER: Liebermeister W 

PROVIDER: S-EPMC1781438 | biostudies-literature | 2006 Dec

REPOSITORIES: biostudies-literature