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BIOMD0000000064 - Teusink2000_Glycolysis

 

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Reference Publication
Publication ID: 10951190
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.
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
Eur. J. Biochem. 2000 Sep; 267(17): 5313-5329
E.C. Slater Institute, BioCentrum Amsterdam, University of Amsterdam, the Netherlands.  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6623915522
Submission Date: 14 Aug 2006 09:05:30 UTC
Last Modification Date: 19 Jul 2012 18:26:07 UTC
Creation Date: 16 Sep 2008 14:00:06 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
   Lukas Endler
set #1
bqbiol:isHomologTo Reactome REACT_723
bqbiol:is KEGG Pathway sce00010
Gene Ontology glycolytic process
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

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.

Model
Publication ID: 10951190 Submission Date: 14 Aug 2006 09:05:30 UTC Last Modification Date: 19 Jul 2012 18:26:07 UTC Creation Date: 16 Sep 2008 14:00:06 UTC
Mathematical expressions
Reactions
Hexokinase Glucose-6-phosphate isomerase Glycogen synthesis Trehalose 6-phosphate synthase
Phosphofructokinase Aldolase Glyceraldehyde 3-phosphate dehydrogenase Phosphoglycerate kinase
Phosphoglycerate mutase Enolase Pyruvate kinase Pyruvate decarboxylase
Succinate synthesis Glucose transport Alcohol dehydrogenase Glycerol 3-phosphate dehydrogenase
ATPase activity      
Rules
Assignment Rule (variable: ADP concentration) Assignment Rule (variable: ATP concentration) Assignment Rule (variable: AMP concentration)  
Physical entities
Compartments Species
extracellular Extracellular Glucose    
cytosol Glucose in Cytosol Glucose 6 Phosphate Fructose 6 Phosphate
Fructose-1,6 bisphosphate Triose-phosphate 1,3-bisphosphoglycerate
3-phosphoglycerate 2-phosphoglycerate Phosphoenolpyruvate
Pyruvate Acetaldehyde High energy phosphates
NAD NADH Glycogen
Trehalose CO2 Succinate
Ethanol Glycerol ATP concentration
ADP concentration AMP concentration sum of AXP conc
F2,6P    
Global parameters
gR KmPFKF6P KmPFKATP Lzero
CiPFKATP KiPFKATP CPFKAMP KPFKAMP
CPFKF26BP KPFKF26BP CPFKF16BP KPFKF16BP
CPFKATP AK eq constant TPI eq constant  
Reactions (17)
 
 Hexokinase [Glucose in Cytosol] + [High energy phosphates] ↔ [Glucose 6 Phosphate];   {ATP concentration} , {ADP concentration}
 
 Glucose-6-phosphate isomerase [Glucose 6 Phosphate] ↔ [Fructose 6 Phosphate];  
 
 Glycogen synthesis [Glucose 6 Phosphate] + [High energy phosphates] → [Glycogen];  
 
 Trehalose 6-phosphate synthase 2.0 × [Glucose 6 Phosphate] + [High energy phosphates] → [Trehalose];  
 
 Phosphofructokinase [Fructose 6 Phosphate] + [High energy phosphates] → [Fructose-1,6 bisphosphate];   {AMP concentration} , {ATP concentration} , {F2,6P}
 
 Aldolase [Fructose-1,6 bisphosphate] ↔ 2.0 × [Triose-phosphate];  
 
 Glyceraldehyde 3-phosphate dehydrogenase [Triose-phosphate] + [NAD] ↔ [1,3-bisphosphoglycerate] + [NADH];  
 
 Phosphoglycerate kinase [1,3-bisphosphoglycerate] ↔ [3-phosphoglycerate] + [High energy phosphates];   {ATP concentration} , {ADP concentration}
 
 Phosphoglycerate mutase [3-phosphoglycerate] ↔ [2-phosphoglycerate];  
 
 Enolase [2-phosphoglycerate] ↔ [Phosphoenolpyruvate];  
 
 Pyruvate kinase [Phosphoenolpyruvate] ↔ [Pyruvate] + [High energy phosphates];   {ATP concentration} , {ADP concentration}
 
 Pyruvate decarboxylase [Pyruvate] → [Acetaldehyde] + [CO2];  
 
 Succinate synthesis 2.0 × [Acetaldehyde] + 3.0 × [NAD] + 4.0 × [High energy phosphates] → 3.0 × [NADH] + [Succinate];  
 
 Glucose transport [Extracellular Glucose] ↔ [Glucose in Cytosol];  
 
 Alcohol dehydrogenase [Acetaldehyde] + [NADH] ↔ [NAD] + [Ethanol];  
 
 Glycerol 3-phosphate dehydrogenase [Triose-phosphate] + [NADH] → [NAD] + [Glycerol];  
 
 ATPase activity [High energy phosphates] ↔ ;   {ATP concentration}
 
Rules (3)
 
 Assignment Rule (name: ADP) ADP concentration = (SUM_P-(P^2*(1-4*KeqAK)+2*SUM_P*P*(4*KeqAK-1)+SUM_P^2)^0.5)/(1-4*KeqAK)
 
 Assignment Rule (name: ATP) ATP concentration = (P-ADP)/2
 
 Assignment Rule (name: AMP) AMP concentration = SUM_P-ATP-ADP
 
Functions (3)
 
 L_PFK lambda(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)
 
 R_PFK lambda(KmF6P, KmATP, g, AT, F6, 1+F6/KmF6P+AT/KmATP+g*F6/KmF6P*AT/KmATP)
 
 T_PFK lambda(CATP, KmATP, AT, 1+CATP*AT/KmATP)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Extracellular Glucose
Compartment: extracellular
Initial concentration: 50.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose in Cytosol
Compartment: cytosol
Initial concentration: 0.087
 
 Glucose 6 Phosphate
Compartment: cytosol
Initial concentration: 2.45
 
 Fructose 6 Phosphate
Compartment: cytosol
Initial concentration: 0.62
 
 Fructose-1,6 bisphosphate
Compartment: cytosol
Initial concentration: 5.51
 
 Triose-phosphate
Compartment: cytosol
Initial concentration: 0.96
 
 1,3-bisphosphoglycerate
Compartment: cytosol
Initial concentration: 0.0
 
 3-phosphoglycerate
Compartment: cytosol
Initial concentration: 0.9
 
 2-phosphoglycerate
Compartment: cytosol
Initial concentration: 0.12
 
 Phosphoenolpyruvate
Compartment: cytosol
Initial concentration: 0.07
 
 Pyruvate
Compartment: cytosol
Initial concentration: 1.85
 
 Acetaldehyde
Compartment: cytosol
Initial concentration: 0.17
 
 High energy phosphates
Compartment: cytosol
Initial concentration: 6.31
 
 NAD
Compartment: cytosol
Initial concentration: 1.2
 
 NADH
Compartment: cytosol
Initial concentration: 0.39
 
 Glycogen
Compartment: cytosol
Initial concentration: 0.0
 
 Trehalose
Compartment: cytosol
Initial concentration: 0.0
 
 CO2
Compartment: cytosol
Initial concentration: 1.0
 
 Succinate
Compartment: cytosol
Initial concentration: 0.0
 
 Ethanol
Compartment: cytosol
Initial concentration: 50.0
 
 Glycerol
Compartment: cytosol
Initial concentration: 0.15
 
  ATP concentration
Compartment: cytosol
 
  ADP concentration
Compartment: cytosol
 
  AMP concentration
Compartment: cytosol
 
 sum of AXP conc
Compartment: cytosol
Initial concentration: 4.1
Constant
 
 F2,6P
Compartment: cytosol
Initial concentration: 0.02
Constant
 
Global Parameters (15)
 
   gR
Value: 5.12   (Units: dimensionless)
Constant
 
   KmPFKF6P
Value: 0.1   (Units: mM)
Constant
 
   KmPFKATP
Value: 0.71   (Units: mM)
Constant
 
   Lzero
Value: 0.66   (Units: dimensionless)
Constant
 
   CiPFKATP
Value: 100.0   (Units: dimensionless)
Constant
 
   KiPFKATP
Value: 0.65   (Units: mM)
Constant
 
   CPFKAMP
Value: 0.0845   (Units: dimensionless)
Constant
 
   KPFKAMP
Value: 0.0995   (Units: mM)
Constant
 
   CPFKF26BP
Value: 0.0174   (Units: dimensionless)
Constant
 
   KPFKF26BP
Value: 6.82E-4   (Units: mM)
Constant
 
   CPFKF16BP
Value: 0.397   (Units: dimensionless)
Constant
 
   KPFKF16BP
Value: 0.111   (Units: mM)
Constant
 
   CPFKATP
Value: 3.0   (Units: dimensionless)
Constant
 
   AK eq constant
Value: 0.45   (Units: dimensionless)
Constant
 
   TPI eq constant
Value: 0.045   (Units: dimensionless)
Constant
 
Hexokinase (6)
 
   VmGLK
Value: 226.452   (Units: mMpermin)
Constant
 
   KmGLKGLCi
Value: 0.08   (Units: mM)
Constant
 
   KmGLKATP
Value: 0.15   (Units: mM)
Constant
 
   KeqGLK
Value: 3800.0   (Units: dimensionless)
Constant
 
   KmGLKG6P
Value: 30.0   (Units: mM)
Constant
 
   KmGLKADP
Value: 0.23   (Units: mM)
Constant
 
Glucose-6-phosphate isomerase (4)
 
   VmPGI_2
Value: 339.677   (Units: mMpermin)
Constant
 
   KmPGIG6P_2
Value: 1.4   (Units: mM)
Constant
 
   KeqPGI_2
Value: 0.314   (Units: dimensionless)
Constant
 
   KmPGIF6P_2
Value: 0.3   (Units: mM)
Constant
 
Glycogen synthesis (1)
 
   KGLYCOGEN_3
Value: 6.0   (Units: mMpermin)
Constant
 
Trehalose 6-phosphate synthase (1)
 
   KTREHALOSE
Value: 2.4   (Units: mMpermin)
Constant
 
Phosphofructokinase (1)
 
   VmPFK
Value: 182.903   (Units: mMpermin)
Constant
 
Aldolase (6)
 
   VmALD
Value: 322.258   (Units: mMpermin)
Constant
 
   KmALDF16P
Value: 0.3   (Units: mM)
Constant
 
   KeqALD
Value: 0.069   (Units: dimensionless)
Constant
 
   KmALDGAP
Value: 2.0   (Units: mM)
Constant
 
   KmALDDHAP
Value: 2.4   (Units: mM)
Constant
 
   KmALDGAPi
Value: 10.0   (Units: mM)
Constant
 
Glyceraldehyde 3-phosphate dehydrogenase (6)
 
   VmGAPDHf
Value: 1184.52   (Units: mMpermin)
Constant
 
   KmGAPDHGAP
Value: 0.21   (Units: mM)
Constant
 
   KmGAPDHNAD
Value: 0.09   (Units: mM)
Constant
 
   VmGAPDHr
Value: 6549.8   (Units: mMpermin)
Constant
 
   KmGAPDHBPG
Value: 0.0098   (Units: mM)
Constant
 
   KmGAPDHNADH
Value: 0.06   (Units: mM)
Constant
 
Phosphoglycerate kinase (6)
 
   VmPGK
Value: 1306.45   (Units: mMpermin)
Constant
 
   KmPGKP3G
Value: 0.53   (Units: mM)
Constant
 
   KmPGKATP
Value: 0.3   (Units: mM)
Constant
 
   KeqPGK
Value: 3200.0   (Units: dimensionless)
Constant
 
   KmPGKBPG
Value: 0.0030   (Units: mM)
Constant
 
   KmPGKADP
Value: 0.2   (Units: mM)
Constant
 
Phosphoglycerate mutase (4)
 
   VmPGM
Value: 2525.81   (Units: mMpermin)
Constant
 
   KmPGMP3G
Value: 1.2   (Units: mM)
Constant
 
   KeqPGM
Value: 0.19   (Units: dimensionless)
Constant
 
   KmPGMP2G
Value: 0.08   (Units: mM)
Constant
 
Enolase (4)
 
   VmENO
Value: 365.806   (Units: mMpermin)
Constant
 
   KmENOP2G
Value: 0.04   (Units: mM)
Constant
 
   KeqENO
Value: 6.7   (Units: dimensionless)
Constant
 
   KmENOPEP
Value: 0.5   (Units: mM)
Constant
 
Pyruvate kinase (6)
 
   VmPYK
Value: 1088.71   (Units: mMpermin)
Constant
 
   KmPYKPEP
Value: 0.14   (Units: mM)
Constant
 
   KmPYKADP
Value: 0.53   (Units: mM)
Constant
 
   KeqPYK
Value: 6500.0   (Units: dimensionless)
Constant
 
   KmPYKPYR
Value: 21.0   (Units: mM)
Constant
 
   KmPYKATP
Value: 1.5   (Units: mM)
Constant
 
Pyruvate decarboxylase (3)
 
   VmPDC
Value: 174.194   (Units: mMpermin)
Constant
 
   nPDC
Value: 1.9   (Units: dimensionless)
Constant
 
   KmPDCPYR
Value: 4.33   (Units: mM)
Constant
 
Succinate synthesis (1)
 
   KSUCC
Value: 21.4
Constant
 
Glucose transport (4)
 
   VmGLT
Value: 97.264   (Units: mmolepermin)
Constant
 
   KmGLTGLCo
Value: 1.1918   (Units: mM)
Constant
 
   KeqGLT
Value: 1.0   (Units: mM)
Constant
 
   KmGLTGLCi
Value: 1.1918   (Units: mM)
Constant
 
Alcohol dehydrogenase (10)
 
   VmADH
Value: 810.0   (Units: mMpermin)
Constant
 
   KiADHNAD
Value: 0.92   (Units: mM)
Constant
 
   KmADHETOH
Value: 17.0   (Units: mM)
Constant
 
   KeqADH
Value: 6.9E-5   (Units: dimensionless)
Constant
 
   KmADHNAD
Value: 0.17   (Units: mM)
Constant
 
   KmADHNADH
Value: 0.11   (Units: mM)
Constant
 
   KiADHNADH
Value: 0.031   (Units: mM)
Constant
 
   KmADHACE
Value: 1.11   (Units: mM)
Constant
 
   KiADHACE
Value: 1.1   (Units: mM)
Constant
 
   KiADHETOH
Value: 90.0   (Units: mM)
Constant
 
Glycerol 3-phosphate dehydrogenase (6)
 
   VmG3PDH
Value: 70.15   (Units: mMpermin)
Constant
 
   KmG3PDHDHAP
Value: 0.4   (Units: mM)
Constant
 
   KmG3PDHNADH
Value: 0.023   (Units: mM)
Constant
 
   KeqG3PDH
Value: 4300.0   (Units: dimensionless)
Constant
 
   KmG3PDHGLY
Value: 1.0   (Units: mM)
Constant
 
   KmG3PDHNAD
Value: 0.93   (Units: mM)
Constant
 
ATPase activity (1)
 
   KATPASE
Value: 33.7   (Units: permin)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000064

Curator's comment: (updated: 21 May 2008 17:47:15 BST)

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.

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