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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 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 : the species a should denote NAD and b Ethanol the last term in the equation should read bpq /( K ib K iq K p ) in the kinetic law for PFK : R = 1 + λ 1 + λ 2 + g r λ 1 λ 2 equation L should read: L = L0*(..) 2 *(..) 2 *(..) …
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initial amount: NaN

metaid_0000032
type: Reaction
is homolog to: REACT 1771
name: Phosphoglycerate kinase
modifier: 773350
modifier: 773338
kinetic law: 773362
reactant: 773302
is: R01512
product: 773326
product: 773314
reversible: true
is: http://identifiers.org/ec-code/2.7.2.3
fast: false

773434
type: LocalParameter
units: metaid_0000072
value: 0.2

773422
type: LocalParameter
units: metaid_0000072
value: 0.003

773410
type: LocalParameter
units: dimensionless
value: 3200.0

773398
type: LocalParameter
units: metaid_0000072
value: 0.3

773386
type: LocalParameter
units: metaid_0000072
value: 0.53

773374
type: LocalParameter
units: metaid_0000084
value: 1306.45

773302
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000009
type: Species
is: CHEBI:16001
initial amount: NaN
in compartment: metaid_0000075
has only substance units: false
name: 1,3-bisphosphoglycerate
is: C00236
constant: false
initial concentration: 0.0
boundary condition: false

773326
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

773314
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000060
type: Parameter
constant: true
units: dimensionless
value: 0.0174

metaid_0000080
type: Parameter
constant: true
units: dimensionless
value: 0.45
name: AK eq constant

metaid_0000029
type: Reaction
is homolog to: REACT 736
kinetic law: 773032
product: 772979
modifier: 772992
reactant: 772953
modifier: 773005
reactant: 772966
name: Phosphofructokinase
reversible: false
modifier: 773018
fast: false
is: R00756
is: http://identifiers.org/ec-code/2.7.1.11

773045
type: LocalParameter
units: metaid_0000084
value: 182.903

772979
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

772953
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

772966
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

metaid_0000031
type: Reaction
reversible: true
product: 773206
reactant: 773170
is homolog to: REACT 1847
is: R01061
kinetic law: 773218
is: http://identifiers.org/ec-code/1.2.1.12
fast: false
reactant: 773182
product: 773194
name: Glyceraldehyde 3-phosphate dehydrogenase

773206
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

773170
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

773290
type: LocalParameter
units: metaid_0000072
value: 0.06

773278
type: LocalParameter
units: metaid_0000072
value: 0.0098

773266
type: LocalParameter
units: metaid_0000084
value: 6549.8

773254
type: LocalParameter
units: metaid_0000072
value: 0.09

773242
type: LocalParameter
units: metaid_0000072
value: 0.21

773230
type: LocalParameter
units: metaid_0000084
value: 1184.52

773182
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

773194
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler

metaid_0000030
type: Reaction
is homolog to: REACT 1602
reversible: true
is: http://identifiers.org/ec-code/4.1.2.13
is: R01070
fast: false
kinetic law: 773084
name: Aldolase
product: 773071
reactant: 773058

773158
type: LocalParameter
units: metaid_0000072
value: 10.0

773146
type: LocalParameter
units: metaid_0000072
value: 2.4

773134
type: LocalParameter
units: metaid_0000072
value: 2.0

773122
type: LocalParameter
units: dimensionless
value: 0.069

773110
type: LocalParameter
units: metaid_0000072
value: 0.3

773097
type: LocalParameter
units: metaid_0000084
value: 322.258

773071
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000008

773058
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

ORG:
  orgname: Stellenbosh University
n:
  given: Jacky L
  family: Snoep

W3 CDTF: Thu Jul 19 19:26:07 BST 2012

W3 CDTF: Tue Sep 16 15:00:06 BST 2008