Teusink2000_Glycolysis

ABSTRACT:

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 _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 .

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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.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Lucian Smith 

PROVIDER: MODEL6623915522 | biostudies-other |

SECONDARY ACCESSION(S): 10951190

REPOSITORIES: biostudies-other