BioModels Database logo

BioModels Database

spacer

BIOMD0000000061 - Hynne2001_Glycolysis

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 11744196
Hynne F, Danø S, Sørensen PG.
Full-scale model of glycolysis in Saccharomyces cerevisiae.
Biophys. Chem. 2001 Dec; 94(1-2): 121-163
Department of Chemistry and CATS, H.C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark. fh@kiku.dk  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6624167348
Submission Date: 20 Jul 2006 22:42:28 UTC
Last Modification Date: 03 Jun 2013 14:20:37 UTC
Creation Date: 12 Jul 2006 07:49:31 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
set #1
bqbiol:is KEGG Pathway Glycolysis / Gluconeogenesis - Saccharomyces cerevisiae (budding yeast)
bqbiol:isVersionOf Gene Ontology glycolytic process
bqbiol:isHomologTo Reactome REACT_1383
set #2
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

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

.

.

.

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

.

.

.

.

.

.

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.

Model
Publication ID: 11744196 Submission Date: 20 Jul 2006 22:42:28 UTC Last Modification Date: 03 Jun 2013 14:20:37 UTC Creation Date: 12 Jul 2006 07:49:31 UTC
Mathematical expressions
Reactions
Glucose Mixed flow to extracellular medium Glucose uptake Hexokinase Phosphoglucoisomerase
Phosphofructokinase Aldolase Triosephosphate isomerase Glyceraldehyde 3-phosphate dehydrogenase
Phosphoenolpyruvate synthesis Pyruvate kinase Pyruvate decarboxylase Alcohol dehydrogenase
Ethanol out Ethanol flow Glycerol synthesis Glycerol out
Glycerol flow Acetaldehyde out Acetaldehyde flow Cyanide-Acetaldehyde flow
Cyanide flow Storage ATP consumption Adenylate kinase
Physical entities
Compartments Species
extracellular Extracellular glucose Extracellular ethanol Extracellular glycerol
Extracellular acetaldehyde Extracellular cyanide P
Mixed flow cyanide Mixed flow glucose  
cytosol Cytosolic glucose ATP Glucose-6-Phosphate
ADP Fructose-6-Phosphate Fructose 1,6-bisphosphate
Glyceraldehyde 3-phosphate Dihydroxyacetone phosphate NAD
1,3-Bisphosphoglycerate NADH Phosphoenolpyruvate
Pyruvate Acetaldehyde EtOH
Glycerol AMP  
Reactions (24)
 
 Glucose Mixed flow to extracellular medium [Mixed flow glucose] ↔ [Extracellular glucose];  
 
 Glucose uptake [Extracellular glucose] ↔ 59.0 × [Cytosolic glucose];   {Glucose-6-Phosphate}
 
 Hexokinase [ATP] + [Cytosolic glucose] ↔ [Glucose-6-Phosphate] + [ADP];  
 
 Phosphoglucoisomerase [Glucose-6-Phosphate] ↔ [Fructose-6-Phosphate];  
 
 Phosphofructokinase [Fructose-6-Phosphate] + [ATP] ↔ [Fructose 1,6-bisphosphate] + [ADP];   {AMP}
 
 Aldolase [Fructose 1,6-bisphosphate] ↔ [Glyceraldehyde 3-phosphate] + [Dihydroxyacetone phosphate];  
 
 Triosephosphate isomerase [Dihydroxyacetone phosphate] ↔ [Glyceraldehyde 3-phosphate];  
 
 Glyceraldehyde 3-phosphate dehydrogenase [Glyceraldehyde 3-phosphate] + [NAD] ↔ [NADH] + [1,3-Bisphosphoglycerate];  
 
 Phosphoenolpyruvate synthesis [1,3-Bisphosphoglycerate] + [ADP] ↔ [Phosphoenolpyruvate] + [ATP];  
 
 Pyruvate kinase [ADP] + [Phosphoenolpyruvate] ↔ [Pyruvate] + [ATP];  
 
 Pyruvate decarboxylase [Pyruvate] ↔ [Acetaldehyde];  
 
 Alcohol dehydrogenase [NADH] + [Acetaldehyde] ↔ [NAD] + [EtOH];  
 
 Ethanol out 59.0 × [EtOH] ↔ [Extracellular ethanol];  
 
 Ethanol flow [Extracellular ethanol] ↔ [P];  
 
 Glycerol synthesis [Dihydroxyacetone phosphate] + [NADH] ↔ [Glycerol] + [NAD];  
 
 Glycerol out 59.0 × [Glycerol] ↔ [Extracellular glycerol];  
 
 Glycerol flow [Extracellular glycerol] ↔ [P];  
 
 Acetaldehyde out 59.0 × [Acetaldehyde] ↔ [Extracellular acetaldehyde];  
 
 Acetaldehyde flow [Extracellular acetaldehyde] ↔ [P];  
 
 Cyanide-Acetaldehyde flow [Extracellular cyanide] + [Extracellular acetaldehyde] ↔ [P];  
 
 Cyanide flow [Mixed flow cyanide] ↔ [Extracellular cyanide];  
 
 Storage [ATP] + [Glucose-6-Phosphate] ↔ [ADP];  
 
 ATP consumption [ATP] ↔ [ADP];  
 
 Adenylate kinase [ATP] + [AMP] ↔ 2.0 × [ADP];  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Extracellular glucose
Compartment: extracellular
Initial concentration: 6.7
 
 Extracellular ethanol
Compartment: extracellular
Initial concentration: 16.4514
 
 Extracellular glycerol
Compartment: extracellular
Initial concentration: 1.68478
 
 Extracellular acetaldehyde
Compartment: extracellular
Initial concentration: 1.28836
 
 Extracellular cyanide
Compartment: extracellular
Initial concentration: 5.20358
 
   P
Compartment: extracellular
Initial concentration: 0.0
 
 Mixed flow cyanide
Compartment: extracellular
Initial concentration: 5.6
 
 Mixed flow glucose
Compartment: extracellular
Initial concentration: 24.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Cytosolic glucose
Compartment: cytosol
Initial concentration: 0.573074
 
 ATP
Compartment: cytosol
Initial concentration: 2.1
 
 Glucose-6-Phosphate
Compartment: cytosol
Initial concentration: 4.2
 
 ADP
Compartment: cytosol
Initial concentration: 1.5
 
 Fructose-6-Phosphate
Compartment: cytosol
Initial concentration: 0.49
 
 Fructose 1,6-bisphosphate
Compartment: cytosol
Initial concentration: 4.64
 
 Glyceraldehyde 3-phosphate
Compartment: cytosol
Initial concentration: 0.115
 
 Dihydroxyacetone phosphate
Compartment: cytosol
Initial concentration: 2.95
 
 NAD
Compartment: cytosol
Initial concentration: 0.65
 
 1,3-Bisphosphoglycerate
Compartment: cytosol
Initial concentration: 2.7E-4
 
 NADH
Compartment: cytosol
Initial concentration: 0.33
 
 Phosphoenolpyruvate
Compartment: cytosol
Initial concentration: 0.04
 
 Pyruvate
Compartment: cytosol
Initial concentration: 8.7
 
 Acetaldehyde
Compartment: cytosol
Initial concentration: 1.48153
 
 EtOH
Compartment: cytosol
Initial concentration: 19.2379
 
 Glycerol
Compartment: cytosol
Initial concentration: 4.196
 
 AMP
Compartment: cytosol
Initial concentration: 0.33
 
Glucose Mixed flow to extracellular medium (1)
 
   k0
Value: 0.048   (Units: minute inverse)
Constant
 
Glucose uptake (7)
 
   V2f
Value: 1014.96   (Units: mM per minute)
Constant
 
   Yvol
Value: 59.0   (Units: dimensionless)
Constant
 
   K2Glc
Value: 1.7   (Units: milliMolar)
Constant
 
   P2
Value: 1.0   (Units: dimensionless)
Constant
 
   K2IG6P
Value: 1.2   (Units: milliMolar)
Constant
 
   K2IIG6P
Value: 7.2   (Units: milliMolar)
Constant
 
   V2r
Value: 1014.96   (Units: mM per minute)
Constant
 
Hexokinase (4)
 
   V3m
Value: 51.7547   (Units: mM per minute)
Constant
 
   K3DGlc
Value: 0.37   (Units: milliMolar)
Constant
 
   K3ATP
Value: 0.1   (Units: milliMolar)
Constant
 
   K3Glc
Constant
 
Phosphoglucoisomerase (5)
 
   V4f
Value: 496.042   (Units: mM per minute)
Constant
 
   K4G6P
Value: 0.8   (Units: milliMolar)
Constant
 
   K4F6P
Value: 0.15   (Units: milliMolar)
Constant
 
   V4r
Value: 496.042   (Units: mM per minute)
Constant
 
   K4eq
Value: 0.13   (Units: dimensionless)
Constant
 
Phosphofructokinase (3)
 
   V5m
Value: 45.4327   (Units: mM per minute)
Constant
 
   K5
Value: 0.021   (Units: mM squared)
Constant
 
   kappa5
Value: 0.15   (Units: dimensionless)
Constant
 
Aldolase (7)
 
   V6f
Value: 2207.82   (Units: mM per minute)
Constant
 
   K6FBP
Value: 0.3   (Units: milliMolar)
Constant
 
   K6DHAP
Value: 2.0   (Units: milliMolar)
Constant
 
   K6eq
Value: 0.081   (Units: milliMolar)
Constant
 
   ratio6
Value: 5.0   (Units: dimensionless)
Constant
 
   K6GAP
Value: 4.0   (Units: milliMolar)
Constant
 
   K6IGAP
Value: 10.0   (Units: milliMolar)
Constant
 
Triosephosphate isomerase (5)
 
   V7f
Value: 116.365   (Units: mM per minute)
Constant
 
   K7DHAP
Value: 1.23   (Units: milliMolar)
Constant
 
   K7GAP
Value: 1.27   (Units: milliMolar)
Constant
 
   V7r
Value: 116.365   (Units: mM per minute)
Constant
 
   K7eq
Value: 0.055   (Units: dimensionless)
Constant
 
Glyceraldehyde 3-phosphate dehydrogenase (7)
 
   V8f
Value: 833.858   (Units: mM per minute)
Constant
 
   K8GAP
Value: 0.6   (Units: milliMolar)
Constant
 
   K8NAD
Value: 0.1   (Units: milliMolar)
Constant
 
   K8BPG
Value: 0.01   (Units: milliMolar)
Constant
 
   K8NADH
Value: 0.06   (Units: milliMolar)
Constant
 
   V8r
Value: 833.858   (Units: mM per minute)
Constant
 
   K8eq
Value: 0.0055   (Units: dimensionless)
Constant
 
Phosphoenolpyruvate synthesis (2)
 
   k9f
Value: 443866.0   (Units: mM inverse min inverse)
Constant
 
   k9r
Value: 1528.62   (Units: mM inverse min inverse)
Constant
 
Pyruvate kinase (3)
 
   V10m
Value: 343.096   (Units: mM per minute)
Constant
 
   K10PEP
Value: 0.2   (Units: milliMolar)
Constant
 
   K10ADP
Value: 0.17   (Units: milliMolar)
Constant
 
Pyruvate decarboxylase (2)
 
   V11m
Value: 53.1328   (Units: mM per minute)
Constant
 
   K11
Value: 0.3   (Units: milliMolar)
Constant
 
Alcohol dehydrogenase (3)
 
   V12m
Value: 89.8023   (Units: mM per minute)
Constant
 
   K12NADH
Value: 0.1   (Units: milliMolar)
Constant
 
   K12ACA
Value: 0.71   (Units: milliMolar)
Constant
 
Ethanol out (2)
 
   k13
Value: 16.72   (Units: minute inverse)
Constant
 
   Yvol
Value: 59.0   (Units: dimensionless)
Constant
 
Ethanol flow (1)
 
   k0
Value: 0.048   (Units: minute inverse)
Constant
 
Glycerol synthesis (5)
 
   V15m
Value: 81.4797   (Units: mM per minute)
Constant
 
   K15DHAP
Value: 25.0   (Units: milliMolar)
Constant
 
   K15INADH
Value: 0.034   (Units: milliMolar)
Constant
 
   K15INAD
Value: 0.13   (Units: milliMolar)
Constant
 
   K15NADH
Value: 0.13   (Units: milliMolar)
Constant
 
Glycerol out (2)
 
   k16
Value: 1.9   (Units: minute inverse)
Constant
 
   Yvol
Value: 59.0   (Units: dimensionless)
Constant
 
Glycerol flow (1)
 
   k0
Value: 0.048   (Units: minute inverse)
Constant
 
Acetaldehyde out (2)
 
   k18
Value: 24.7   (Units: minute inverse)
Constant
 
   Yvol
Value: 59.0   (Units: dimensionless)
Constant
 
Acetaldehyde flow (1)
 
   k0
Value: 0.048   (Units: minute inverse)
Constant
 
Cyanide-Acetaldehyde flow (1)
 
   k20
Value: 0.00283828   (Units: mM inverse min inverse)
Constant
 
Cyanide flow (1)
 
   k0
Value: 0.048   (Units: minute inverse)
Constant
 
Storage (1)
 
   k22
Value: 2.25932   (Units: mM inverse min inverse)
Constant
 
ATP consumption (1)
 
   k23
Value: 3.2076   (Units: minute inverse)
Constant
 
Adenylate kinase (2)
 
   k24f
Value: 432.9   (Units: mM inverse min inverse)
Constant
 
   k24r
Value: 133.333   (Units: mM inverse min inverse)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000061

Curator's comment: (updated: 21 Mar 2013 14:36:10 GMT)

Figure 6 of the reference publication is reproduced using Copasi v4.8 (Build 35).

spacer
spacer