public model
Model Identifier
BIOMD0000000064
Short description

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 
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 ib K iq K 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 .


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Format
SBML (L2V1)
Related Publication
  • Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
  • Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL
  • European journal of biochemistry , 9/ 2000 , Volume 267 , pages: 5313-5329 , PubMed ID: 10951190
  • E.C. Slater Institute, BioCentrum Amsterdam, University of Amsterdam, the Netherlands.
  • This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured. In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.
Contributors
Nicolas Le Novère

Metadata information

isDescribedBy
PubMed 10951190
hasTaxon
isHomologTo

Curation status
Curated

Original model(s)
http://jjj.biochem.sun.ac.za/database/teusink/index.html

Tags
Name Description Size Actions

Model files

BIOMD0000000064_url.xml SBML L2V1 representation of Teusink2000_Glycolysis 99.95 KB Preview | Download

Additional files

BIOMD0000000064.m Auto-generated Octave file 19.94 KB Preview | Download
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BIOMD0000000064.xpp Auto-generated XPP file 14.31 KB Preview | Download
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BIOMD0000000064_urn.xml Auto-generated SBML file with URNs 105.97 KB Preview | Download

  • Model originally submitted by : Nicolas Le Novère
  • Submitted: 14-Aug-2006 10:05:30
  • Last Modified: 19-Jul-2012 19:26:07
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 19-Jul-2012 19:26:07
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Teusink2000_Glycolysis
  • Version: 1 public model Download this version
    • Submitted on: 14-Aug-2006 10:05:30
    • Submitted by: Nicolas Le Novère
    • With comment: Original import of Teusink2000_Glycolysis

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Reactions
Reactions Rate Parameters
TRIO + NADH => NAD + GLY 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)) KmG3PDHGLY=1.0 mM; KeqG3PDH=4300.0 dimensionless; KmG3PDHDHAP=0.4 mM; KmG3PDHNADH=0.023 mM; KeqTPI = 0.045 dimensionless; KmG3PDHNAD=0.93 mM; VmG3PDH=70.15 mMpermin
G6P + P => Trh cytosol*KTREHALOSE KTREHALOSE=2.4 mMpermin
ACE + NAD + P => NADH + SUCC cytosol*KSUCC*ACE KSUCC=21.4
AMP = (SUM_P-ATP)-ADP [] []
GLCi + P => G6P; ATP, ADP cytosol*VmGLK/(KmGLKGLCi*KmGLKATP)*(GLCi*ATP-G6P*ADP/KeqGLK)/((1+GLCi/KmGLKGLCi+G6P/KmGLKG6P)*(1+ATP/KmGLKATP+ADP/KmGLKADP)) KmGLKADP=0.23 mM; KmGLKGLCi=0.08 mM; VmGLK=226.452 mMpermin; KmGLKG6P=30.0 mM; KeqGLK=3800.0 dimensionless; KmGLKATP=0.15 mM
G6P => F6P cytosol*VmPGI_2/KmPGIG6P_2*(G6P-F6P/KeqPGI_2)/(1+G6P/KmPGIG6P_2+F6P/KmPGIF6P_2) KmPGIG6P_2=1.4 mM; VmPGI_2=339.677 mMpermin; KmPGIF6P_2=0.3 mM; KeqPGI_2=0.314 dimensionless
F6P + P => F16P; AMP, ATP, F26BP 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) KPFKF26BP = 6.82E-4 mM; KmPFKF6P = 0.1 mM; CiPFKATP = 100.0 dimensionless; CPFKATP = 3.0 dimensionless; CPFKAMP = 0.0845 dimensionless; KPFKF16BP = 0.111 mM; Lzero = 0.66 dimensionless; VmPFK=182.903 mMpermin; CPFKF26BP = 0.0174 dimensionless; CPFKF16BP = 0.397 dimensionless; KPFKAMP = 0.0995 mM; gR = 5.12 dimensionless; KiPFKATP = 0.65 mM; KmPFKATP = 0.71 mM
GLCo => GLCi VmGLT/KmGLTGLCo*(GLCo-GLCi/KeqGLT)/(1+GLCo/KmGLTGLCo+GLCi/KmGLTGLCi+0.91*GLCo*GLCi/(KmGLTGLCo*KmGLTGLCi)) KeqGLT=1.0 mM; KmGLTGLCo=1.1918 mM; VmGLT=97.264 mmolepermin; KmGLTGLCi=1.1918 mM
G6P + P => Glyc cytosol*KGLYCOGEN_3 KGLYCOGEN_3=6.0 mMpermin
F16P => TRIO 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)) KmALDGAP=2.0 mM; VmALD=322.258 mMpermin; KeqALD=0.069 dimensionless; KmALDDHAP=2.4 mM; KeqTPI = 0.045 dimensionless; KmALDGAPi=10.0 mM; KmALDF16P=0.3 mM
Curator's comment:
(added: 21 May 2008, 17:47:15, updated: 21 May 2008, 17:47:15)
The steady state results calculated with copasi v4.4(b26) The value for G6P might be a misprint in the publication, as the JWS version of the model also gives 1.03 mM.