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dupreez7

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v_ACEclear

∅ = ACE

v_ADH

ACE + NADH = NAD

v_ADPclear

∅ = ADP

v_AK

{2.0}ADP = AMP + ATP

v_ALD

F16P = {2.0}TRIO

v_AMPclear

∅ = AMP

v_ATP

ATP = ADP

v_ATPclear

∅ = ATP

v_BPGclear

∅ = BPG

v_ENO

P2G = PEP

v_F16Pclear

∅ = F16P

v_F6Pclear

∅ = F6P

v_G3PA

G3P = ∅

v_G3PDH

NADH + TRIO = G3P + NAD

v_G3Pclear

∅ = G3P

v_G6Pclear

∅ = G6P

v_GAPDH

NAD + TRIO = BPG + NADH

v_GLCiclear

∅ = GLCi

v_GLK

ATP + GLCi = ADP + G6P

v_GLYCO

ATP + G6P = ADP

v_NADHclear

∅ = NADH

v_NADclear

∅ = NAD

v_P2Gclear

∅ = P2G

v_P3Gclear

∅ = P3G

v_PDC

PYR = ACE

v_PEPclear

∅ = PEP

v_PFK

ATP + F6P = ADP + F16P

v_PGI

G6P = F6P

v_PGK

ADP + BPG = ATP + P3G

v_PGM

P3G = P2G

v_PYK

ADP + PEP = ATP + PYR

v_PYRclear

∅ = PYR

v_SUC

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

v_TRIOclear

∅ = TRIO

v_Treha

ATP + {2.0}G6P = ADP

Parameters

Global parameters

ACEwashin*

ADPmedium*

AKopt*

AMPmedium*

ATPmedium*

BPGwashin*

CPFKAMP*

CPFKATP*

CPFKF16BP*

CPFKF26BP*

CiPFKATP*

ETOH*

EXTERNAL*

F16Pwashin*

F26BP*

F6Pwashin*

G3Pwashin*

G6Pwashin*

GLCmedium*

KATPASE*

KGLYCOGEN*

KPFKAMP*

KPFKF16BP*

KPFKF26BP*

KSUCC*

KTREHALOSE*

KeqADH*

KeqAK*

KeqALD*

KeqENO*

KeqG3PDH*

KeqGAPDH*

KeqGLK*

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*

KmPDCPYR*

KmPFKATP*

KmPFKF6P*

KmPGIF6P*

KmPGIG6P*

KmPGKADP*

KmPGKATP*

KmPGKBPG*

KmPGKP3G*

KmPGMP2G*

KmPGMP3G*

KmPYKADP*

KmPYKATP*

KmPYKPEP*

KmPYKPYR*

L0*

NADHmedium*

NADmedium*

P2Gwashin*

P3Gwashin*

PEPwashin*

PYRwashin*

Phi*

TRIOwashin*

VmADH*

VmALD*

VmENO*

VmG3PA*

VmG3PDH*

VmGAPDHf*

VmGLK*

VmGLT*

VmPDC*

VmPFK*

VmPGI*

VmPGK*

VmPGM*

VmPYK*

biomassFac*

ccWashInConcMult*

gR*

k0*

nATP*

nPDC*

default_compartment*

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 compartments*

Gravity*

Repulsion*

Pool threshold*

Species:

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Model schema*

Start time*

End time*

log scales

y-axis min/max

x-axis min/max

Species

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Assignment rules

Parameter*

Start*

End*

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

v_ACEclear
v_ADH
v_ADPclear
v_AK
v_ALD
v_AMPclear
v_ATP
v_ATPclear
v_BPGclear
v_ENO
v_F16Pclear
v_F6Pclear
v_G3PA
v_G3PDH
v_G3Pclear
v_G6Pclear
v_GAPDH
v_GLCiclear
v_GLK
v_GLYCO
v_NADHclear
v_NADclear
v_P2Gclear
v_P3Gclear
v_PDC
v_PEPclear
v_PFK
v_PGI
v_PGK
v_PGM
v_PYK
v_PYRclear
v_SUC
v_TRIOclear
v_Treha