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BIOMD0000000063 - Galazzo1990_FermentationPathwayKinetics

 

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Reference Publication
Publication ID: 10.1016/0141-0229(90...
Jorge L. Galazzo and James E. Bailey
Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae
Enzyme and Microbial Technology 1990; 12(3): 162-172
Department of Chemical Engineering, California Institute of Technology, Pasadena, CA, USA  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6624154196
Submission Date: 14 Aug 2006 09:03:42 UTC
Last Modification Date: 02 Apr 2014 00:54:05 UTC
Creation Date: 13 Aug 2006 19:32:16 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
   Lukas Endler
set #1
bqbiol:hasPart Gene Ontology glycolytic process
set #2
bqbiol:isVersionOf Gene Ontology glycolytic fermentation
bqbiol:is KEGG Pathway Glycolysis / Gluconeogenesis - Saccharomyces cerevisiae (budding yeast)
bqbiol:isHomologTo Reactome REACT_723
set #3
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
set #4
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

This a model from the article:
Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae
Jorge L. Galazzo and James E. Bailey Enzyme and Microbial TechnologyVolume 12, Issue 3, 1990, Pages 162-172.
DOI:10.1016/0141-0229(90)90033-M
Abstract:
Measurements of rates of glucose uptake and of glycerol and ethanol formation combined with knowledge of the metabolic pathways involved in S. cerevisiae were employed to obtain in vivo rates of reaction catalysed by pathway enzymes for suspended and alginate-entrapped cells at pH 4.5 and 5.5. Intracellular concentrations of substrates and effectors for most key pathway enzymes were estimated from in vivo phosphorus-31 nuclear magnetic resonance measurements. These data show the validity in vivo of kinetic models previously proposed for phosphofructokinase and pyruvate kinase based on in vitro studies. Kinetic representations of hexokinase, glycogen synthetase, and glyceraldehyde 3-phosphate dehydrogenase, which incorporate major regulatory properties of these enzymes, are all consistent with the in vivo data. This detailed model of pathway kinetics and these data on intracellular metabolite concentrations allow evaluation of flux-control coefficients for all key enzymes involved in glucose catabolism under the four different cell environments examined. This analysis indicates that alginate entrapment increases the glucose uptake rate and shifts the step most influencing ethanol production from glucose uptake to phosphofructokinase. The rate of ATP utilization in these nongrowing cells strongly limits ethanol production at pH 5.5 but is relatively insignificant at pH 4.5.

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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Biomodels Curation: The model reproduces Fig 2 of the paper. However, it appears that the figures are swapped, hence the plot for V/Vmax vs Glucose actually represnts V/Vmax vs ATP and the vice versa is true for the other figure. The rate of hexokinase reaction that is obtained upon simulation of the model is 17.24 mM/min, therefore V/Vmax has a value of 17.24/68.5=0.25. For steady state values of Glucose and ATP (0.038 and 1.213 mM respectively), the V/Vmax values correctly correspond to 0.25, if we were to assume that the figures are swapped.

BioModels Curation updated on 25th November 2010: Figure 3 of the reference publication has been reproduced and added as a curation figure for the model.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
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.

Model
Publication ID: 10.1016/0141-0229(90... Submission Date: 14 Aug 2006 09:03:42 UTC Last Modification Date: 02 Apr 2014 00:54:05 UTC Creation Date: 13 Aug 2006 19:32:16 UTC
Mathematical expressions
Reactions
Glucose in Hexokinase Trehalose and Glycogen formation Phosphofructokinase
GAPD Pyruvate kinase Glycerol synthesis ATPase
Rules
Assignment Rule (variable: VappGly) Assignment Rule (variable: VratioVmax_ATP)    
Physical entities
Compartments Species
Extracellular Glucose outside the cell    
Cytoplasm Glucose inside the cell ATP Glucose 6-phosphate
Fructose 1,6-phosphate Phosphoenol pyruvate Glycerol
Ethanol Glycogen and Trehalose  
Global parameters
VappGly VratioVmax_ATP Trehalose and Glycogen formation_Vm3 Trehalose and Glycogen formation_n3
Trehalose and Glycogen formation_K3Gly Hexokinase_Vm2    
Reactions (8)
 
 Glucose in [Glucose outside the cell] ↔ [Glucose inside the cell];   {Glucose 6-phosphate}
 
 Hexokinase [ATP] + [Glucose inside the cell] ↔ [Glucose 6-phosphate];  
 
 Trehalose and Glycogen formation [ATP] + [Glucose 6-phosphate] ↔ [Glycogen and Trehalose];  
 
 Phosphofructokinase [ATP] + [Glucose 6-phosphate] ↔ [Fructose 1,6-phosphate];  
 
 GAPD [Fructose 1,6-phosphate] ↔ 2.0 × [ATP] + 2.0 × [Phosphoenol pyruvate];  
 
 Pyruvate kinase [Phosphoenol pyruvate] ↔ [ATP] + [Ethanol];   {Fructose 1,6-phosphate}
 
 Glycerol synthesis 0.5 × [Fructose 1,6-phosphate] ↔ [Glycerol];   {Phosphoenol pyruvate} , {ATP}
 
 ATPase [ATP] ↔ ;  
 
Rules (2)
 
 Assignment Rule (name: VappGly) VappGly = parameter_4*G6P^parameter_5/(parameter_6^parameter_5+G6P^parameter_5)
 
 Assignment Rule (name: VratioVmax) VratioVmax_ATP = Vhk/(cytoplasm*parameter_7)
 
 Extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose outside the cell
Compartment: Extracellular
Initial concentration: 1.0
 
 Cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose inside the cell
Compartment: Cytoplasm
Initial concentration: 0.0345
 
 ATP
Compartment: Cytoplasm
Initial concentration: 1.19
 
 Glucose 6-phosphate
Compartment: Cytoplasm
Initial concentration: 1.011
 
 Fructose 1,6-phosphate
Compartment: Cytoplasm
Initial concentration: 9.144
 
 Phosphoenol pyruvate
Compartment: Cytoplasm
Initial concentration: 0.0095
 
 Glycerol
Compartment: Cytoplasm
Initial concentration: 0.0
 
 Ethanol
Compartment: Cytoplasm
Initial concentration: 0.0
 
 Glycogen and Trehalose
Compartment: Cytoplasm
Initial concentration: 0.0
 
Global Parameters (6)
 
   VappGly
Value: NaN   (Units: mM per minute)
 
   VratioVmax_ATP
Value: NaN   (Units: dimensionless)
 
   Trehalose and Glycogen formation_Vm3
Value: 14.31   (Units: mM per minute)
Constant
 
   Trehalose and Glycogen formation_n3
Value: 8.25   (Units: dimensionless)
Constant
 
   Trehalose and Glycogen formation_K3Gly
Value: 2.0   (Units: milliMolar)
Constant
 
   Hexokinase_Vm2
Value: 68.5   (Units: mM per minute)
Constant
 
Glucose in (2)
 
   Vm1
Value: 19.7   (Units: mM per minute)
Constant
 
   Ki1G6P
Value: 3.7   (Units: minute_inverse)
Constant
 
Hexokinase (4)
 
   Vm2
Value: 68.5   (Units: mM per minute)
Constant
 
   Km2Glc
Value: 0.11   (Units: milliMolar)
Constant
 
   Km2ATP
Value: 0.1   (Units: milliMolar)
Constant
 
   Ks2Glc
Value: 0.0062   (Units: milliMolar)
Constant
 
Trehalose and Glycogen formation (5)
 
   Vm3
Value: 14.31   (Units: mM per minute)
Constant
 
   n3
Value: 8.25   (Units: dimensionless)
Constant
 
   K3Gly
Value: 2.0   (Units: milliMolar)
Constant
 
   Km30
Value: 1.0   (Units: milliMolar)
Constant
 
   Km3G6P
Value: 1.1   (Units: milliMolar)
Constant
 
Phosphofructokinase (10)
 
   Vm4
Value: 31.7   (Units: mM per minute)
Constant
 
   g4R
Value: 10.0   (Units: dimensionless)
Constant
 
   K4F6P
Value: 1.0   (Units: milliMolar)
Constant
 
   K4ATP
Value: 0.06   (Units: milliMolar)
Constant
 
   L40
Value: 3342.0   (Units: dimensionless)
Constant
 
   c4AMP
Value: 0.019   (Units: dimensionless)
Constant
 
   K4AMP
Value: 0.025   (Units: milliMolar)
Constant
 
   c4F6P
Value: 5.0E-4   (Units: dimensionless)
Constant
 
   c4ATP
Value: 1.0   (Units: dimensionless)
Constant
 
   gT
Value: 1.0   (Units: dimensionless)
Constant
 
GAPD (9)
 
   Vm5
Value: 49.9   (Units: mM per minute)
Constant
 
   K5G3P
Value: 0.0025   (Units: milliMolar)
Constant
 
   K5NAD
Value: 0.18   (Units: dimensionless)
Constant
 
   NAD
Value: 1.91939   (Units: milliMolar)
Constant
 
   NADH
Value: 0.0806142   (Units: milliMolar)
Constant
 
   K5NADH
Value: 3.0E-4   (Units: milliMolar)
Constant
 
   K5ADP
Value: 1.5   (Units: milliMolar)
Constant
 
   K5AMP
Value: 1.1   (Units: milliMolar)
Constant
 
   K5ATP
Value: 2.5   (Units: milliMolar)
Constant
 
Pyruvate kinase (12)
 
   Vm6
Value: 3440.0   (Units: mM per minute)
Constant
 
   K6PEP
Value: 0.00793966   (Units: milliMolar)
Constant
 
   K6ADP
Value: 5.0   (Units: milliMolar)
Constant
 
   g6R
Value: 0.1   (Units: dimensionless)
Constant
 
   q6
Value: 1.0   (Units: dimensionless)
Constant
 
   L60
Value: 164.084   (Units: dimensionless)
Constant
 
   c6FDP
Value: 0.01   (Units: dimensionless)
Constant
 
   K6FDP
Value: 0.2   (Units: milliMolar)
Constant
 
   g6T
Value: 1.0   (Units: dimensionless)
Constant
 
   c6PEP
Value: 1.58793E-4   (Units: dimensionless)
Constant
 
   c6ADP
Value: 1.0   (Units: dimensionless)
Constant
 
   h6
Value: 1.14815E-7   (Units: dimensionless)
Constant
 
Glycerol synthesis (12)
 
   Vm7
Value: 203.0   (Units: mM per minute)
Constant
 
   K6PEP
Value: 0.00793966   (Units: milliMolar)
Constant
 
   K6ADP
Value: 5.0   (Units: milliMolar)
Constant
 
   g6R
Value: 0.1   (Units: dimensionless)
Constant
 
   q6
Value: 1.0   (Units: dimensionless)
Constant
 
   L60
Value: 164.084   (Units: dimensionless)
Constant
 
   c6FDP
Value: 0.01   (Units: dimensionless)
Constant
 
   K6FDP
Value: 0.2   (Units: milliMolar)
Constant
 
   g6T
Value: 1.0   (Units: dimensionless)
Constant
 
   c6PEP
Value: 1.58793E-4   (Units: dimensionless)
Constant
 
   c6ADP
Value: 1.0   (Units: dimensionless)
Constant
 
   h6
Value: 1.14815E-7   (Units: dimensionless)
Constant
 
ATPase (1)
 
   Vm8
Value: 25.1   (Units: minute_inverse)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000063

Curator's comment: (updated: 20 Apr 2011 00:04:30 BST)

Reproduction of figure 3 of the reference publication using Copasi v4.6 (Build 33). For this figure, Glucose-6-phosphate was set fixed and its initial concentration varied over the given interval (0-5 mM). Steady state was calculated by integrating a time course for 1000 minutes.

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