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
, Bioinformatics, 20:2143-2144
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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.
Submitter of this revision: Nicolas Le Novère
Modellers: Nicolas Le Novère
Metadata information
BioModels Database BIOMD0000000061
KEGG Pathway Glycolysis / Gluconeogenesis - Saccharomyces cerevisiae (budding yeast)
Connected external resources
SBGN view in Newt Editor
| 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-biopax2.owl | Auto-generated BioPAX (Level 2) | 61.92 KB | Preview | Download |
| BIOMD0000000061-biopax3.owl | Auto-generated BioPAX (Level 3) | 88.32 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.png | Auto-generated Reaction graph (PNG) | 215.04 KB | Preview | Download |
| BIOMD0000000061.sci | Auto-generated Scilab file | 214.00 Bytes | Preview | Download |
| BIOMD0000000061.svg | Auto-generated Reaction graph (SVG) | 51.22 KB | Preview | Download |
| BIOMD0000000061.vcml | Auto-generated VCML file | 98.64 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 |
- Model originally submitted by : Nicolas Le Novère
- Submitted: Jul 20, 2006 11:42:28 PM
- Last Modified: Jun 3, 2013 3:20:37 PM
Revisions
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Version: 2
- Submitted on: Jun 3, 2013 3:20:37 PM
- Submitted by: Nicolas Le Novère
- With comment: Current version of Hynne2001_Glycolysis
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Version: 1
- Submitted on: Jul 20, 2006 11:42:28 PM
- 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
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: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| NAD NAD(+) ; NAD+ |
0.65 mmol |
| PEP Phosphoenolpyruvate ; phosphoenolpyruvate ; phosphoenolpyruvate |
0.04 mmol |
| GlcX0 glucose ; C00293 |
24.0 mmol |
| CNX cyanide ; Cyanide ion |
5.20358 mmol |
| ADP ADP ; ADP |
1.5 mmol |
| NADH NADH ; NADH |
0.33 mmol |
| ACA acetaldehyde ; Acetaldehyde |
1.48153 mmol |
| EtOHX ethanol ; C000469 |
16.4514 mmol |
| P | 0.0 mmol |
| Reactions | Rate | Parameters |
|---|---|---|
| GAP + NAD => NADH + BPG | cytosol*(V8f*GAP*NAD/K8GAP/K8NAD/((1+GAP/K8GAP+BPG/K8BPG)*(1+NAD/K8NAD+NADH/K8NADH))-V8r*BPG*NADH/K8eq/K8GAP/K8NAD/((1+GAP/K8GAP+BPG/K8BPG)*(1+NAD/K8NAD+NADH/K8NADH))) | K8NADH=0.06 milliMolar; K8GAP=0.6 milliMolar; V8r=833.858 mM per minute; K8NAD=0.1 milliMolar; V8f=833.858 mM per minute; K8eq=0.0055 dimensionless; K8BPG=0.01 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 |
| GlcX0 => GlcX | extracellular*k0*(GlcX0-GlcX) | k0=0.048 minute inverse |
| CNX + ACAX => P | extracellular*k20*ACAX*CNX | k20=0.00283828 mM inverse min inverse |
| 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 |
| 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 |
| Pyr => ACA | cytosol*V11m*Pyr/(K11+Pyr) | V11m=53.1328 mM per minute; K11=0.3 milliMolar |
| EtOH => EtOHX | k13/Yvol*(cytosol*EtOH-extracellular*EtOHX) | Yvol=59.0 dimensionless; k13=16.72 minute inverse |
| BPG + ADP => PEP + ATP | cytosol*(k9f*BPG*ADP-k9r*PEP*ATP) | k9r=1528.62 mM inverse min inverse; k9f=443866.0 mM inverse min 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)