Hynne2001_Glycolysis
The model reproduces Fig 6 of the paper. The stoichiometry and rate of reactions involving uptake of metabolites from extracellular medium have been changed corresponding to Yvol (ratio of extracellular volume to cytosolic volume) mentioned in the publication. The extracellular and cytosolic compartments have been set to 1. Concentration of extracellular glucose, GlcX, is set to 6.7 according to the equation for cellular glucose uptake rate in Table 7 of the paper. The model was successfully tested on MathSBML and Jarnac
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SBML
level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based
modelling using JWS Online
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This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use
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To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
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Full-scale model of glycolysis in Saccharomyces cerevisiae.
- Hynne F, Danø S, Sørensen PG
- Biophysical chemistry , 12/ 2001 , Volume 94 , pages: 121-163 , PubMed ID: 11744196
- Department of Chemistry and CATS, H.C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark. fh@kiku.dk
- We present a powerful, general method of fitting a model of a biochemical pathway to experimental substrate concentrations and dynamical properties measured at a stationary state, when the mechanism is largely known but kinetic parameters are lacking. Rate constants and maximum velocities are calculated from the experimental data by simple algebra without integration of kinetic equations. Using this direct approach, we fit a comprehensive model of glycolysis and glycolytic oscillations in intact yeast cells to data measured on a suspension of living cells of Saccharomyces cerevisiae near a Hopf bifurcation, and to a large set of stationary concentrations and other data estimated from comparable batch experiments. The resulting model agrees with almost all experimentally known stationary concentrations and metabolic fluxes, with the frequency of oscillation and with the majority of other experimentally known kinetic and dynamical variables. The functional forms of the rate equations have not been optimized.
Metadata information
BioModels Database BIOMD0000000061
KEGG Pathway Glycolysis / Gluconeogenesis - Saccharomyces cerevisiae (budding yeast)
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000061_url.xml | SBML L2V1 representation of Hynne2001_Glycolysis | 86.66 KB | Preview | Download |
Additional files |
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| BIOMD0000000061.vcml | Auto-generated VCML file | 98.64 KB | Preview | Download |
| BIOMD0000000061.png | Auto-generated Reaction graph (PNG) | 215.04 KB | Preview | Download |
| BIOMD0000000061.xpp | Auto-generated XPP file | 11.84 KB | Preview | Download |
| BIOMD0000000061_urn.xml | Auto-generated SBML file with URNs | 91.45 KB | Preview | Download |
| BIOMD0000000061.svg | Auto-generated Reaction graph (SVG) | 51.22 KB | Preview | Download |
| BIOMD0000000061.m | Auto-generated Octave file | 17.84 KB | Preview | Download |
| BIOMD0000000061.pdf | Auto-generated PDF file | 276.02 KB | Preview | Download |
| BIOMD0000000061.sci | Auto-generated Scilab file | 214.00 Bytes | Preview | Download |
| BIOMD0000000061-biopax3.owl | Auto-generated BioPAX (Level 3) | 88.32 KB | Preview | Download |
| BIOMD0000000061-biopax2.owl | Auto-generated BioPAX (Level 2) | 61.92 KB | Preview | Download |
- Model originally submitted by : Nicolas Le Novère
- Submitted: 20-Jul-2006 23:42:28
- Last Modified: 03-Jun-2013 15:20:37
Revisions
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Version: 2
- Submitted on: 03-Jun-2013 15:20:37
- Submitted by: Nicolas Le Novère
- With comment: Current version of Hynne2001_Glycolysis
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Version: 1
- Submitted on: 20-Jul-2006 23:42:28
- Submitted by: Nicolas Le Novère
- With comment: Original import of hynne
(*) You might be seeing discontinuous
revisions as only public revisions are displayed here. Any private revisions
of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| Glc glucose ; C00293 |
0.573074 mmol |
| ATP ATP ; ATP |
2.1 mmol |
| G6P aldehydo-D-glucose 6-phosphate ; D-Glucose 6-phosphate |
4.2 mmol |
| P | 0.0 mmol |
| CNX0 cyanide ; Cyanide ion |
5.6 mmol |
| NAD NAD(+) ; NAD+ |
0.65 mmol |
| NADH NADH ; NADH |
0.33 mmol |
| PEP Phosphoenolpyruvate ; phosphoenolpyruvate ; phosphoenolpyruvate |
0.04 mmol |
| Pyr pyruvate ; Pyruvate ; pyruvic acid |
8.7 mmol |
| ACA acetaldehyde ; Acetaldehyde |
1.48153 mmol |
| EtOH ethanol ; Ethanol |
19.2379 mmol |
| EtOHX ethanol ; C000469 |
16.4514 mmol |
| Glyc glycerol ; Glycerol |
4.196 mmol |
| Reactions | Rate | Parameters |
|---|---|---|
| ATP + Glc => G6P + ADP | cytosol*V3m*ATP*Glc/(K3DGlc*K3ATP+K3Glc*ATP+K3ATP*Glc+Glc*ATP) | K3DGlc=0.37 milliMolar; K3Glc=0.0 milliMolar; V3m=51.7547 mM per minute; K3ATP=0.1 milliMolar |
| ATP + G6P => ADP | cytosol*k22*ATP*G6P | k22=2.25932 mM inverse min inverse |
| G6P => F6P | cytosol*(V4f*G6P/(K4G6P+G6P+K4G6P/K4F6P*F6P)-V4r*F6P/K4eq/(K4G6P+G6P+K4G6P/K4F6P*F6P)) | K4F6P=0.15 milliMolar; V4f=496.042 mM per minute; V4r=496.042 mM per minute; K4G6P=0.8 milliMolar; K4eq=0.13 dimensionless |
| GlycX => P | extracellular*k0*GlycX | k0=0.048 minute inverse |
| ACAX => P | extracellular*k0*ACAX | k0=0.048 minute inverse |
| CNX0 => CNX | extracellular*k0*(CNX0-CNX) | k0=0.048 minute inverse |
| DHAP + NADH => Glyc + NAD | cytosol*V15m*DHAP/(K15DHAP*(1+K15INADH/NADH*(1+NAD/K15INAD))+DHAP*(1+K15NADH/NADH*(1+NAD/K15INAD))) | K15NADH=0.13 milliMolar; K15INADH=0.034 milliMolar; V15m=81.4797 mM per minute; K15DHAP=25.0 milliMolar; K15INAD=0.13 milliMolar |
| ADP + PEP => Pyr + ATP | cytosol*V10m*ADP*PEP/((K10PEP+PEP)*(K10ADP+ADP)) | K10PEP=0.2 milliMolar; V10m=343.096 mM per minute; K10ADP=0.17 milliMolar |
| Pyr => ACA | cytosol*V11m*Pyr/(K11+Pyr) | V11m=53.1328 mM per minute; K11=0.3 milliMolar |
| ACA => ACAX | k18/Yvol*(cytosol*ACA-extracellular*ACAX) | Yvol=59.0 dimensionless; k18=24.7 minute inverse |
| EtOH => EtOHX | k13/Yvol*(cytosol*EtOH-extracellular*EtOHX) | Yvol=59.0 dimensionless; k13=16.72 minute inverse |
| EtOHX => P | extracellular*k0*EtOHX | k0=0.048 minute inverse |
(added: 21 Mar 2013, 14:36:10, updated: 21 Mar 2013, 14:36:10)