Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
Teusink,B et al.: Eur J Biochem 2000 Sep;267(17):5313-29.
The model reproduces the steady-state fluxes and metabolite concentrations of the branched model as given in Table 4 of the paper. It is derived from the model on JWS online, but has the ATP consumption in the succinate branch with the same stoichiometrie as in the publication. The model was successfully tested on copasi v.4.4(build 26).
For Vmax values, please note that there is a conversion factor of approx. 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol). The equilibrium constant for the ADH reaction in the paper is given for the reverse reaction (Keq = 1.45*10 4). The value used in this model is for the forward reaction: 1/Keq = 6.9*10 -5 .
Vmax parameters values used (in [mM/min] except VmGLT):
VmGLT 97.264 mmol/min
VmGLK 226.45
VmPGI 339.667
VmPFK 182.903
VmALD 322.258
VmGAPDH_f 1184.52
VmGAPDH_r 6549.68
VmPGK 1306.45
VmPGM 2525.81
VmENO 365.806
VmPYK 1088.71
VmPDC 174.194
VmG3PDH 70.15
The result of the G6P steady state concentration (marked in red) differs slightly from the one given in table 4. of the publication
Results for steady state:
orig. article this model
Fluxes[mM/min] 
Glucose  88  88 
Ethanol  129  129 
Glycogen  6  6 
Trehalose  4.8  4.8  (G6P flux through trehalose branch)
Glycerol  18.2  18.2 
Succinate  3.6  3.6 
Conc.[mM] 
G6P  1.07  1.03 
F6P  0.11  0.11 
F1,6P  0.6  0.6 
DHAP  0.74  0.74 
3PGA  0.36  0.36 
2PGA  0.04  0.04 
PEP  0.07  0.07 
PYR  8.52  8.52 
AcAld  0.17  0.17 
ATP  2.51  2.51 
ADP  1.29  1.29 
AMP  0.3  0.3 
NAD  1.55  1.55 
NADH  0.04  0.04 
Authors of the publication also mentioned a few misprints in the original article:
in the kinetic law for ADH:

  1. the species a should denote NAD and b Ethanol
  2. the last term in the equation should read bpq/( K ibK iqK p )
in the kinetic law for PFK:
  1. R = 1 + λ 1 + λ 2 + g r λ 1 λ 2
  2. equation L should read: L = L0*(..) 2*(..) 2*(..) 2 not L = L0*(..) 2*(..) 2*(..)
To make the model easier to curate, the species ATP, ADP and AMP were added. These are calculated via assignment rules from the active phosphate species, P, and the sum of all AXP, SUM_P.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Snoep Jacky L jls@sun.ac.za Stellenbosh University Dharuri Harish hdharuri@cds.caltech.edu California Institute of Technology Endler Lukas lukas@ebi.ac.uk EMBL-EBI 2008-09-16T14:00:06Z 2010-01-27T16:06:41Z L CiATP KiATP CAMP KAMP CF26BP KF26BP CF16BP KF16BP AT AM F16 F26 L 1 CiATP AT KiATP 1 AT KiATP 2 1 CAMP AM KAMP 1 AM KAMP 2 1 CF26BP F26 KF26BP CF16BP F16 KF16BP 1 F26 KF26BP F16 KF16BP 2 KmF6P KmATP g AT F6 1 F6 KmF6P AT KmATP g F6 KmF6P AT KmATP CATP KmATP AT 1 CATP AT KmATP SUM_P P 2 1 4 KeqAK 2 SUM_P P 4 KeqAK 1 SUM_P 2 0.5 1 4 KeqAK P ADP 2 SUM_P ATP ADP cytosol VmGLK KmGLKGLCi KmGLKATP GLCi ATP G6P ADP KeqGLK 1 GLCi KmGLKGLCi G6P KmGLKG6P 1 ATP KmGLKATP ADP KmGLKADP cytosol VmPGI_2 KmPGIG6P_2 G6P F6P KeqPGI_2 1 G6P KmPGIG6P_2 F6P KmPGIF6P_2 cytosol KGLYCOGEN_3 cytosol KTREHALOSE cytosol VmPFK gR F6P KmPFKF6P ATP KmPFKATP R_PFK KmPFKF6P KmPFKATP gR ATP F6P R_PFK KmPFKF6P KmPFKATP gR ATP F6P 2 L_PFK Lzero CiPFKATP KiPFKATP CPFKAMP KPFKAMP CPFKF26BP KPFKF26BP CPFKF16BP KPFKF16BP ATP AMP F16P F26BP T_PFK CPFKATP KmPFKATP ATP 2 cytosol VmALD KmALDF16P F16P KeqTPI 1 KeqTPI TRIO 1 1 KeqTPI TRIO KeqALD 1 F16P KmALDF16P KeqTPI 1 KeqTPI TRIO KmALDGAP 1 1 KeqTPI TRIO KmALDDHAP KeqTPI 1 KeqTPI TRIO 1 1 KeqTPI TRIO KmALDGAP KmALDDHAP F16P KeqTPI 1 KeqTPI TRIO KmALDGAPi KmALDF16P cytosol VmGAPDHf KeqTPI 1 KeqTPI TRIO NAD KmGAPDHGAP KmGAPDHNAD VmGAPDHr BPG NADH KmGAPDHBPG KmGAPDHNADH 1 KeqTPI 1 KeqTPI TRIO KmGAPDHGAP BPG KmGAPDHBPG 1 NAD KmGAPDHNAD NADH KmGAPDHNADH cytosol VmPGK KmPGKP3G KmPGKATP KeqPGK BPG ADP P3G ATP 1 BPG KmPGKBPG P3G KmPGKP3G 1 ATP KmPGKATP ADP KmPGKADP cytosol VmPGM KmPGMP3G P3G P2G KeqPGM 1 P3G KmPGMP3G P2G KmPGMP2G cytosol VmENO KmENOP2G P2G PEP KeqENO 1 P2G KmENOP2G PEP KmENOPEP cytosol VmPYK KmPYKPEP KmPYKADP PEP ADP PYR ATP KeqPYK 1 PEP KmPYKPEP PYR KmPYKPYR 1 ATP KmPYKATP ADP KmPYKADP cytosol VmPDC PYR nPDC KmPDCPYR nPDC 1 PYR nPDC KmPDCPYR nPDC cytosol KSUCC ACE VmGLT KmGLTGLCo GLCo GLCi KeqGLT 1 GLCo KmGLTGLCo GLCi KmGLTGLCi 0.91 GLCo GLCi KmGLTGLCo KmGLTGLCi cytosol VmADH KiADHNAD KmADHETOH NAD ETOH NADH ACE KeqADH 1 NAD KiADHNAD KmADHNAD ETOH KiADHNAD KmADHETOH KmADHNADH ACE KiADHNADH KmADHACE NADH KiADHNADH NAD ETOH KiADHNAD KmADHETOH KmADHNADH NAD ACE KiADHNAD KiADHNADH KmADHACE KmADHNAD ETOH NADH KiADHNAD KmADHETOH KiADHNADH NADH ACE KiADHNADH KmADHACE NAD ETOH ACE KiADHNAD KmADHETOH KiADHACE ETOH NADH ACE KiADHETOH KiADHNADH KmADHACE cytosol VmG3PDH KmG3PDHDHAP KmG3PDHNADH 1 1 KeqTPI TRIO NADH GLY NAD KeqG3PDH 1 1 1 KeqTPI TRIO KmG3PDHDHAP GLY KmG3PDHGLY 1 NADH KmG3PDHNADH NAD KmG3PDHNAD cytosol KATPASE ATP