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 |
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 |
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 )
- R = 1 + λ 1 + λ 2 + g r λ 1 λ 2
- equation L should read: L = L0*(..) 2 *(..) 2 *(..) 2 not L = L0*(..) 2 *(..) 2 *(..)
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.
-
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.
Submitter of this revision: Nicolas Le Novère
Modellers: Nicolas Le Novère
Metadata information
BioModels Database MODEL6623915522
BioModels Database BIOMD0000000064
Gene Ontology glycolytic process
Connected external resources
Name | Description | Size | Actions |
---|---|---|---|
Model files |
|||
BIOMD0000000064_url.xml | SBML L2V1 representation of Teusink2000_Glycolysis | 99.95 KB | Preview | Download |
Additional files |
|||
BIOMD0000000064-biopax2.owl | Auto-generated BioPAX (Level 2) | 58.07 KB | Preview | Download |
BIOMD0000000064-biopax3.owl | Auto-generated BioPAX (Level 3) | 79.52 KB | Preview | Download |
BIOMD0000000064.m | Auto-generated Octave file | 19.94 KB | Preview | Download |
BIOMD0000000064.pdf | Auto-generated PDF file | 692.31 KB | Preview | Download |
BIOMD0000000064.png | Auto-generated Reaction graph (PNG) | 222.74 KB | Preview | Download |
BIOMD0000000064.sci | Auto-generated Scilab file | 181.00 Bytes | Preview | Download |
BIOMD0000000064.svg | Auto-generated Reaction graph (SVG) | 44.42 KB | Preview | Download |
BIOMD0000000064.vcml | Auto-generated VCML file | 118.32 KB | Preview | Download |
BIOMD0000000064.xpp | Auto-generated XPP file | 14.31 KB | Preview | Download |
BIOMD0000000064_urn.xml | Auto-generated SBML file with URNs | 105.97 KB | Preview | Download |
- Model originally submitted by : Nicolas Le Novère
- Submitted: Aug 14, 2006 10:05:30 AM
- Last Modified: Jul 19, 2012 7:26:07 PM
Revisions
-
Version: 2
- Submitted on: Jul 19, 2012 7:26:07 PM
- Submitted by: Nicolas Le Novère
- With comment: Current version of Teusink2000_Glycolysis
-
Version: 1
- Submitted on: Aug 14, 2006 10:05:30 AM
- Submitted by: Nicolas Le Novère
- With comment: Original import of Teusink2000_Glycolysis
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revisions as only public revisions are displayed here. Any private revisions
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: Variable used inside SBML models
Species | Initial Concentration/Amount |
---|---|
BPG 3-phospho-D-glyceroyl dihydrogen phosphate ; 3-Phospho-D-glyceroyl phosphate |
0.0 mmol |
F16P keto-D-fructose 1,6-bisphosphate ; D-Fructose 1,6-bisphosphate |
5.51 mmol |
G6P alpha-D-glucose 6-phosphate ; alpha-D-Glucose 6-phosphate |
2.45 mmol |
P ADP ; ATP ; ADP ; ADP ; ATP |
6.31 mmol |
NAD NAD(+) ; NAD+ |
1.2 mmol |
GLCo glucose ; C00293 |
50.0 mmol |
NADH NADH ; NADH |
0.39 mmol |
GLY glycerol ; Glycerol |
0.15 mmol |
Reactions | Rate | Parameters |
---|---|---|
TRIO + NAD => BPG + NADH | 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)) | VmGAPDHf=1184.52 mMpermin; VmGAPDHr=6549.8 mMpermin; KmGAPDHNAD=0.09 mM; KmGAPDHBPG=0.0098 mM; KmGAPDHGAP=0.21 mM; KeqTPI = 0.045 dimensionless; KmGAPDHNADH=0.06 mM |
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 |
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 |
G6P + P => Glyc | cytosol*KGLYCOGEN_3 | KGLYCOGEN_3=6.0 mMpermin |
ACE + NADH => NAD + ETOH | (-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)) | KmADHNAD=0.17 mM; KiADHETOH=90.0 mM; KiADHNADH=0.031 mM; KiADHACE=1.1 mM; KmADHETOH=17.0 mM; KeqADH=6.9E-5 dimensionless; KmADHNADH=0.11 mM; KiADHNAD=0.92 mM; VmADH=810.0 mMpermin; KmADHACE=1.11 mM |
G6P + P => Trh | cytosol*KTREHALOSE | KTREHALOSE=2.4 mMpermin |
BPG => P3G + P; ATP, ADP | cytosol*VmPGK/(KmPGKP3G*KmPGKATP)*(KeqPGK*BPG*ADP-P3G*ATP)/((1+BPG/KmPGKBPG+P3G/KmPGKP3G)*(1+ATP/KmPGKATP+ADP/KmPGKADP)) | KmPGKBPG=0.003 mM; KmPGKATP=0.3 mM; KeqPGK=3200.0 dimensionless; VmPGK=1306.45 mMpermin; KmPGKP3G=0.53 mM; KmPGKADP=0.2 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 |
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 |
(added: 21 May 2008, 17:47:15, updated: 21 May 2008, 17:47:15)