v_1
Glco = Glc
v_10
EtOH = P
v_11
ACA = P
v_12
Pyr = P
v_13
PEP = P
v_14
BPG = P
v_15
GAP = P
v_16
FBP = P
v_17
F6P = P
v_18
F6P = P
v_19
Glc = P
v_2
Glc + ATP = F6P + ADP
v_20
NADo = NAD
v_21
NAD = P
v_22
NADHo = NADH
v_23
NADH = P
v_24
ADPo = ADP
v_25
ADP = P
v_26
ATPo = ATP
v_27
ATP = P
v_28
AMP = P
v_29
AMP + ATP = {2.0}ADP
v_3
v_3
F6P + ATP = FBP + ADP
v_4
FBP = {2.0}GAP
v_5
GAP + NAD = BPG + NADH
v_6
BPG + ADP = PEP + ATP
v_7
PEP + ADP = Pyr + ATP
v_8
Pyr = ACA
v_9
ACA + NADH = EtOH + NAD
Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.
Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations.
Biophys. Chem. 1998;
72
:
49
- PubMed: 17029704
- ISSN: 0301-4622
- URL: http://ncbi.nlm.nih.gov/pubmed/17029704
Abstract
We report sustained oscillations in glycolysis conducted in an open system (a continuous-flow, stirred tank reactor; CSTR) with inflow of yeast extract as well as glucose. Depending on the operating conditions, we observe simple or complex periodic oscillations or chaos. We report the response of the system to instantaneous additions of small amounts of several substrates as functions of the amount added and the phase of the addition. We simulate oscillations and perturbations by a kinetic model based on the mechanism of glycolysis in a CSTR. We find that the response to particular perturbations forms an efficient tool for elucidating the mechanism of biochemical oscillations.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000042).
Biomodels notes: "Figure 9d of the paper reproduced using COPASI 4.8 (build 35)."
JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. The following additional figures were reproduced: Figure 9A, 9B, and 9C. In order to reproduce these Figures the parameter V4m was changed from 20 mM to 10 mM. The time that is modelled is from 150 to 330 minutes rather than 0 to 180 minutes (as this is when the limit cycle is stable).