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dupreez1

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v_ADH

ACE + NADH = NAD

v_AK

{2.0}ADP = AMP + ATP

v_ALD

F16P = {2.0}TRIO

v_ATP

ATP = ADP

v_ENO

P2G = PEP

v_G3PA

G3P = ∅

v_G3PDH

NADH + TRIO = G3P + NAD

v_GAPDH

NAD + TRIO = BPG + NADH

v_GLK

ATP + GLCi = ADP + G6P

v_GLT

∅ = GLCi

v_GLYCO

ATP + G6P = ADP

v_PDC

PYR = ACE

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_SUC

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

v_Treha

ATP + {2.0}G6P = ADP

Parameters

Global parameters

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*

Phi*

VmADH*

VmALD*

VmENO*

VmG3PA*

VmG3PDH*

VmGAPDHf*

VmGLK*

VmGLT*

VmPDC*

VmPFK*

VmPGI*

VmPGK*

VmPGM*

VmPYK*

alpha*

gR*

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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Gravity*

Repulsion*

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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.

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