Fung2005_Metabolic_Oscillator

A Synthetic Gene-Metabolic Oscillator
Reference:

Fung et al; Nature (2005) 435:118-122

Name of kinetic law
Reaction

Glycolytic flux, V_gly:
nil -> AcCoA;

Flux to TCA cycle/ETOH, V_TCA:
AcCoA -> TCA/EtOH;

HOAc ex/import,reversible, V_out:
HOAc -> HOAc_E

V_Pta:
AcCoA + Pi -> AcP + CoA

reversible, V_Ack:
AcP + ADP -> OAc + ATP

V_Acs:
OAC + ATP -> AcCoA +PPi

Acetic acid-base equillibrium, reversible, V_Ace:
OAC + H -> HOAc

Expression of LacI, R_LacI:
nil -> LacI

Expression of Acs, R_Acs:
nil -> Acs

Expression of Pta, R_Pta:
nil -> Pta

LacI degradation, R_dLacI:
LacI -> nil

Acs degradation, R_dAcs:
Acs -> nil

Pta degradation, R_dPta:
Pta -> nil

For this model the differential equation for V_Ace was changed from:
C*(AcP*H-K_eq*OAC) with C = 100 in the supplemental material
to C*(OAc*H-K_eq*HOAc) with C = 100, as in
Bulter et. al; PNAS(2004),101,2299-2304

, and a value for K_eq of 5*10^-4 after communication with the authors.

translated to SBML by:
Lukas Endler(luen at tbi.univie.ac.at), Christoph Flamm (xtof at tbi.univie.ac.at)

Biomodels Curation
The model reproduces 3a of the paper for glycolytic flux Vgly = 0.5. The authors have agreed that the values on Y-axis are marked wrong and hence there is a discrepancy between model simulation results and the figure. Also, note that the values of concentration and time are in dimensionless units. The model was successfully tested on MathSBML and Jarnac.