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dupreez5

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v_ACEinflow

∅ = ACEo

v_ACEt

ACE = {0.02}ACEo

v_ADH

ACE + NADH = ∅

v_AK

∅ = AMP + ATP

v_ALD

F16P = {2.0}TRIO

v_ATP

ATP = ∅

v_CNinflow

∅ = CNreactor

v_ENO

P2G = PEP

v_G3PA

G3P = ∅

v_G3PDH

NADH + TRIO = G3P

v_GAPDH

TRIO = BPG + NADH

v_GLCinflow

∅ = GLCreactor

v_GLK

ATP + GLCi = G6P

v_GLT

{0.02}GLCreactor = GLCi

v_GLYCO

ATP + G6P = ∅

v_LACTO

ACEo + CNreactor = ∅

v_PDC

PYR = ACE

v_PFK

ATP + F6P = F16P

v_PGI

G6P = F6P

v_PGK

BPG = ATP + P3G

v_PGM

P3G = P2G

v_PYK

PEP = ATP + PYR

v_SUC

{2.0}ACE + {4.0}ATP = {3.0}NADH

v_Treha

ATP + {2.0}G6P = ∅

Parameters

Global parameters

ACEmedium*

AKopt*

AXPsum*

CNmedium*

CPFKAMP*

CPFKATP*

CPFKF16BP*

CPFKF26BP*

CiPFKATP*

ETOH*

EXTERNAL*

F26BP*

GLCmedium*

KATPASE*

KGLYCOGEN*

KPFKAMP*

KPFKF16BP*

KPFKF26BP*

KSUCC*

KTREHALOSE*

KeqADH*

KeqAK*

KeqALD*

KeqENO*

KeqG3PDH*

KeqGAPDH*

KeqGLK*

KeqGLT*

KeqPGI*

KeqPGK*

KeqPGM*

KeqPYK*

KeqTPI*

KiADHACE*

KiADHETOH*

KiADHNAD*

KiADHNADH*

KiPFKATP*

KmADHACE*

KmADHETOH*

KmADHNAD*

KmADHNADH*

KmALDDHAP*

KmALDF16P*

KmALDGAP*

KmALDGAPi*

KmATP*

KmENOP2G*

KmENOPEP*

KmG3PAG3P*

KmG3PAPhi*

KmG3PDHADP*

KmG3PDHATP*

KmG3PDHDHAP*

KmG3PDHF16P*

KmG3PDHG3P*

KmG3PDHNAD*

KmG3PDHNADH*

KmGAPDHBPG*

KmGAPDHGAP*

KmGAPDHNAD*

KmGAPDHNADH*

KmGLKADP*

KmGLKATP*

KmGLKG6P*

KmGLKGLCi*

KmGLTGLCi*

KmGLTGLCo*

KmPDCPYR*

KmPFKATP*

KmPFKF6P*

KmPGIF6P*

KmPGIG6P*

KmPGKADP*

KmPGKATP*

KmPGKBPG*

KmPGKP3G*

KmPGMP2G*

KmPGMP3G*

KmPYKADP*

KmPYKATP*

KmPYKPEP*

KmPYKPYR*

L0*

NADSUM*

Phi*

VmADH*

VmALD*

VmENO*

VmG3PA*

VmG3PDH*

VmGAPDHf*

VmGLK*

VmGLT*

VmPDC*

VmPFK*

VmPGI*

VmPGK*

VmPGM*

VmPYK*

alpha*

gR*

k0*

kACEt*

kLACTO*

nATP*

nPDC*

optACEt*

optLACTO*

yvol*

default_compartment*

Functions and Rules

Assignment rules

ADP = AXPsum - AMP - ATP

NAD = NADSUM - NADH

Function definitions

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.

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Show modifiers*

Show compartments*

Gravity*

Repulsion*

Pool threshold*

Species:

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Model schema*

Parameter*

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Steps*

Species

Rates

Assignment rules

From steady-state to synchronized yeast glycolytic oscillations II: model validation.

Franco B du Preez
David D van Niekerk
Jacky L Snoep

FEBS J. 2012; 279 (16): 2823-2836

PubMed: 22686585
DOI: 10.1111/j.1742-4658.2012.08658.x
ISSN: 1742-4658
URL: http://ncbi.nlm.nih.gov/pubmed/22686585

Abstract

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we validate the model by testing its capacity to simulate a wide range of experiments on dynamics of yeast glycolysis. In addition to its description of the oscillations of glycolytic intermediates in intact cells and the rapid synchronization observed when mixing out-of-phase oscillatory cell populations (see accompanying paper), the model was able to predict the Hopf bifurcation diagram with glucose as the bifurcation parameter (and one of the bifurcation points with cyanide as the bifurcation parameter), the glucose- and acetaldehyde-driven forced oscillations, glucose and acetaldehyde quenching, and cell-free extract oscillations (including complex oscillations and mixed-mode oscillations). Thus, the model was compliant, at least qualitatively, with the majority of available experimental data for glycolytic oscillations in yeast. To our knowledge, this is the first time that a model for yeast glycolysis has been tested against such a wide variety of independent data sets.
DATABASE: The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/dupreez/index.html.

No additional notes are available for this model.

JWS Online documentation

dupreez5

Reactions

v_ACEinflow

v_ACEt

v_ADH

v_AK

v_ALD

v_ATP

v_CNinflow

v_ENO

v_G3PA

v_G3PDH

v_GAPDH

v_GLCinflow

v_GLK

v_GLT

v_GLYCO

v_LACTO

v_PDC

v_PFK

v_PGI

v_PGK

v_PGM

v_PYK

v_SUC

v_Treha

Parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

Function definitions

Events

Constraints

From steady-state to synchronized yeast glycolytic oscillations II: model validation.

Abstract

v_ACEinflow
v_ACEt
v_ADH (v_ADH)
v_AK (v_AK)
v_ALD
v_ATP
v_CNinflow
v_ENO
v_G3PA
v_G3PDH (v_G3PDH)
v_GAPDH (v_GAPDH)
v_GLCinflow
v_GLK (v_GLK)
v_GLT
v_GLYCO
v_LACTO
v_PDC
v_PFK
v_PGI
v_PGK (v_PGK)
v_PGM
v_PYK (v_PYK)
v_SUC
v_Treha