Hynne2001_Glycolysis

  public model
Model Identifier
BIOMD0000000061
Short description

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 .
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.

Format
SBML (L2V1)
Related Publication
  • 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.
Contributors
Submitter of the first revision: Nicolas Le Novère
Submitter of this revision: Nicolas Le Novère
Modellers: Nicolas Le Novère

Metadata information

isDescribedBy
PubMed 11744196
hasTaxon
isVersionOf
Gene Ontology glycolytic process
isHomologTo
Reactome Glycolysis

Curation status
Curated

Original model(s)
http://jjj.biochem.sun.ac.za/database/hynne/index.html

Tags

Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

BIOMD0000000061_url.xml SBML L2V1 representation of Hynne2001_Glycolysis 86.66 KB Preview | Download

Additional files

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
  • Version: 2 public model Download this version
    • Submitted on: Jun 3, 2013 3:20:37 PM
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Hynne2001_Glycolysis
  • Version: 1 public model Download this version
    • 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 unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
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
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
Curator's comment:
(added: 21 Mar 2013, 14:36:10, updated: 21 Mar 2013, 14:36:10)
Figure 6 of the reference publication is reproduced using Copasi v4.8 (Build 35).