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dupreez3

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v_ADH

ACE + NADH = ∅

v_AK

∅ = AMP + ATP

v_ALD

F16P = {2.0}TRIO

v_ATP

ATP = ∅

v_ENO

P2G = PEP

v_G3PA

G3P = ∅

v_G3PDH

NADH + TRIO = G3P

v_GAPDH

TRIO = BPG + NADH

v_GLK

ATP + GLCi = G6P

v_GLT

∅ = GLCi

v_GLYCO

ATP + G6P = ∅

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

AKopt*

AXPsum*

CPFKAMP*

CPFKATP*

CPFKF16BP*

CPFKF26BP*

CiPFKATP*

ETOH*

EXTERNAL*

F26BP*

GLCo*

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*

biomassFac*

gR*

nATP*

nPDC*

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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Gravity*

Repulsion*

Pool threshold*

Species:

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Model schema*

Parameter*

Start*

End*

Steps*

Species

Rates

Assignment rules

From steady-state to synchronized yeast glycolytic oscillations I: model construction.

Franco B du Preez
David D van Niekerk
Bob Kooi
Johann M Rohwer
Jacky L Snoep

FEBS J. 2012; 279 (16): 2810-2822

PubMed: 22712534
DOI: 10.1111/j.1742-4658.2012.08665.x
ISSN: 1742-4658
URL: http://ncbi.nlm.nih.gov/pubmed/22712534

Abstract

UNLABELLED: An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original model was adapted by adjusting its parameter values in three optimization steps. Only small adaptations to the original model were required for realistic simulation of experimental data for limit-cycle oscillations. The greatest changes were required for parameter values for the phosphofructokinase reaction. The importance of ATP for the oscillatory mechanism and NAD(H) for inter-and intra-cellular communications and synchronization was evident in the optimization steps and simulation experiments. In an accompanying paper [du Preez F et al. (2012) FEBS J279, 2823-2836], we validate the model for a wide variety of experiments on oscillatory yeast cells. The results are important for re-use of detailed kinetic models in modular modeling approaches and for approaches such as that used in the Silicon Cell initiative.
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

dupreez3

Reactions

v_ADH

v_AK

v_ALD

v_ATP

v_ENO

v_G3PA

v_G3PDH

v_GAPDH

v_GLK

v_GLT

v_GLYCO

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 I: model construction.

Abstract