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BIOMD0000000281 - Chance1960_Glycolysis_Respiration

 

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Reference Publication
Publication ID: 13692276
CHANCE B, GARFINKEL D, HIGGINS J, HESS B.
Metabolic control mechanisms. 5. A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells.
J. Biol. Chem. 1960 Aug; 235: 2426-2439
  [more]
Model
Original Model: BIOMD0000000281.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1010190002
Submission Date: 19 Oct 2010 11:34:06 UTC
Last Modification Date: 16 Mar 2011 03:53:21 UTC
Creation Date: 10 Oct 2010 10:10:10 UTC
Encoders:  Lukas Endler
   Kieran Smallbone
set #1
bqbiol:isVersionOf Gene Ontology glycolytic process
Gene Ontology oxidative phosphorylation
bqbiol:hasVersion Reactome REACT_1383.6
set #2
bqbiol:hasVersion KEGG Pathway hsa00010
bqbiol:occursIn Taxonomy Homo sapiens
Brenda Tissue Ontology BTO:0000094
Notes

This model is described inthe article:
Metabolic control mechanisms. 5. A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells.
Britton Chance, David Garfinkel, Joseph Higgins and Benno Hess, J Biol Chem. 1960 35:2426-2439. PubmedID: 13692276
Abstract:
The other papers of this series present experimental evidence for possible relationships between the kinetics of oxygen, glucose, adenosine diphosphate, adenosine triphosphate, and phosphate and those of the cytochromes and pyridine nucleotides of the ascites tumor cell. From these general experiments we are able to formulate, under the law of mass action, a minimum hypothesis under which the four metabolic regulations previously described can be observed. In brief, the system can be represented by the known enzyme systems, a relatively higher ADP affinity in respiration than in glycolysis, the mitochondrial membrane, a segregation of ATP into two compartments, and an ATP-utilizing system that is responsive to small decreases of the intracellular ADP level. The chemical equations for the pathway from glucose to oxygen are solved by a digital computer method so that the responses of the chemical equations and of the living cell can be accurately compared.
For reasons already described, we greatly prefer a com- puter representation based upon a physical or chemical law representing the action of the system to a model simulating the operation of the chemical system but not based upon funda- mental laws for the reactions involved; such a representation would not adequately represent the kinetics of the system, as in an electric circuit network or in some types of hydraulic ana- logues.

The model gives solutions of the reaction kinetics for three types of metabolism:

  1. 0 - 64s, metabolism of endogenous substrate
  2. 64s - 119s, metabolism of added glucose, illustrating the activated and inhibited aspects of glucose metabolism
  3. 119s - 153s, relief of glucose and oxygen inhibition by the addition of an uncoupling agent

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: 13692276 Submission Date: 19 Oct 2010 11:34:06 UTC Last Modification Date: 16 Mar 2011 03:53:21 UTC Creation Date: 10 Oct 2010 10:10:10 UTC
Mathematical expressions
Reactions
reaction 1 reaction 2 reaction 3 reaction 4
reaction 5 reaction 6 reaction 7 reaction 8
reaction 9 reaction 10 reaction 11 reaction 12
reaction 13 reaction 14 reaction 15 reaction 16
reaction 17 reaction 18 reaction 19 reaction 20
reaction 21 reaction 22    
Rules
Assignment Rule (variable: relative GLU) Assignment Rule (variable: relative ENZ) Assignment Rule (variable: relative ENG) Assignment Rule (variable: relative TP1)
Assignment Rule (variable: relative ADP) Assignment Rule (variable: relative GLP) Assignment Rule (variable: relative ETZ) Assignment Rule (variable: relative ETG)
Assignment Rule (variable: relative GPP) Assignment Rule (variable: relative GAP) Assignment Rule (variable: relative DHA) Assignment Rule (variable: relative DPN)
Assignment Rule (variable: relative DPH) Assignment Rule (variable: relative PID) Assignment Rule (variable: relative DGA) Assignment Rule (variable: relative PGA)
Assignment Rule (variable: relative PYR) Assignment Rule (variable: relative LAC) Assignment Rule (variable: relative DIN) Assignment Rule (variable: relative DIH)
Assignment Rule (variable: relative XI) Assignment Rule (variable: relative XSI) Assignment Rule (variable: relative OXY) Assignment Rule (variable: relative XSP)
Assignment Rule (variable: relative TP2) Assignment Rule (variable: relative DBP) Assignment Rule (variable: relative PUE) Assignment Rule (variable: relative PPP)
Assignment Rule (variable: relative AGP) Assignment Rule (variable: relative MOD) Assignment Rule (variable: relative MOB) Assignment Rule (variable: relative MOX)
Events
addition of glucose addition of uncoupling agent    
Physical entities
Compartments Species
cell (GLU) glucose (ENZ) hexokinase (ENG) hexokinase-glucose intermediate
(TP1) adenosine triphosphate in store 1 (cytoplasm) (ADP) adenosine diphosphate (GLP) glucose 6-phosphate
(ETZ) phosphofructokinase (ETG) phosphofructokinase intermediate (GPP) hexose diphosphate
(GAP) glyceraldehyde 3-phosphate (DHA) dihydroxacetone phosphate (DPN) extramitochondrial diphospyridine nucleotide
(DPH) extramitochondrial reduced diphospyridine nucleotide (PID) inorganic phosphate (DGA) 1,3 diphosphoglycerate
(PGA) 3 phosphoglycerate (PYR) pyruvate (LAC) lactate
(DIN) intramitochondrial diphospyridine nucleotide (DIH) intramitochondrial reduced diphospyridine nucleotide (XI) low energy intermediate in oxidative phosphorylation
(XSI) high energy intermediate in oxidative phosphorylation (OXY) oxygen (XSP) phosphorylated intermediate in oxidative phosphorylation
(TP2) adenosine triphosphate in store 2 (mitochondria) (DBP) dibromophenol (PUE) enzyme concerned in ATP utilization
(PPP) enzyme intermediate concerned in ATP utilization (AGP) alpha-glycerophosphate (MOD) glyceraldehyde 3-phoshphate dehydrogenase-DPN complex
(MOB) acyl enzyme intermediate of glyceraldehyde 3-phoshphate dehydrogenase (MOX) glyceraldehyde 3-phoshphate dehydrogenase  
Global parameters
relative GLU relative ENZ relative ENG relative TP1
relative ADP relative GLP relative ETZ relative ETG
relative GPP relative GAP relative DHA relative DPN
relative DPH relative PID relative DGA relative PGA
relative PYR relative LAC relative DIN relative DIH
relative XI relative XSI relative OXY relative XSP
relative TP2 relative DBP relative PUE relative PPP
relative AGP relative MOD relative MOB relative MOX
Reactions (22)
 
 reaction 1 [(GLU) glucose] + [(ENZ) hexokinase] → [(ENG) hexokinase-glucose intermediate];  
 
 reaction 2 [(ENG) hexokinase-glucose intermediate] + [(TP1) adenosine triphosphate in store 1 (cytoplasm)] → [(ADP) adenosine diphosphate] + [(GLP) glucose 6-phosphate] + [(ENZ) hexokinase];  
 
 reaction 3 [(GLP) glucose 6-phosphate] + [(ETZ) phosphofructokinase] → [(ETG) phosphofructokinase intermediate];  
 
 reaction 4 [(ETG) phosphofructokinase intermediate] + [(TP1) adenosine triphosphate in store 1 (cytoplasm)] → [(GPP) hexose diphosphate] + [(ETZ) phosphofructokinase] + [(ADP) adenosine diphosphate];  
 
 reaction 5 [(GPP) hexose diphosphate] → [(GAP) glyceraldehyde 3-phosphate] + [(DHA) dihydroxacetone phosphate];  
 
 reaction 6 [(DHA) dihydroxacetone phosphate] + [(DPH) extramitochondrial reduced diphospyridine nucleotide] → [(AGP) alpha-glycerophosphate] + [(DPN) extramitochondrial diphospyridine nucleotide];  
 
 reaction 7 [(AGP) alpha-glycerophosphate] + [(DPN) extramitochondrial diphospyridine nucleotide] → [(DHA) dihydroxacetone phosphate] + [(DPH) extramitochondrial reduced diphospyridine nucleotide];  
 
 reaction 8 [(GAP) glyceraldehyde 3-phosphate] + [(MOD) glyceraldehyde 3-phoshphate dehydrogenase-DPN complex] → [(MOB) acyl enzyme intermediate of glyceraldehyde 3-phoshphate dehydrogenase] + [(DPH) extramitochondrial reduced diphospyridine nucleotide];  
 
 reaction 9 [(MOB) acyl enzyme intermediate of glyceraldehyde 3-phoshphate dehydrogenase] + [(PID) inorganic phosphate] → [(DGA) 1,3 diphosphoglycerate] + [(MOX) glyceraldehyde 3-phoshphate dehydrogenase];  
 
 reaction 10 [(MOX) glyceraldehyde 3-phoshphate dehydrogenase] + [(DPN) extramitochondrial diphospyridine nucleotide] → [(MOD) glyceraldehyde 3-phoshphate dehydrogenase-DPN complex];  
 
 reaction 11 [(DGA) 1,3 diphosphoglycerate] + [(ADP) adenosine diphosphate] → [(TP1) adenosine triphosphate in store 1 (cytoplasm)] + [(PGA) 3 phosphoglycerate];  
 
 reaction 12 [(PGA) 3 phosphoglycerate] + [(ADP) adenosine diphosphate] → [(TP1) adenosine triphosphate in store 1 (cytoplasm)] + [(PYR) pyruvate];  
 
 reaction 13 [(PYR) pyruvate] + [(DPH) extramitochondrial reduced diphospyridine nucleotide] → [(LAC) lactate] + [(DPN) extramitochondrial diphospyridine nucleotide];  
 
 reaction 14 [(LAC) lactate] + [(DPN) extramitochondrial diphospyridine nucleotide] → [(PYR) pyruvate] + [(DPH) extramitochondrial reduced diphospyridine nucleotide];  
 
 reaction 15 [(PYR) pyruvate] + 4.0 × [(DIN) intramitochondrial diphospyridine nucleotide] → 4.0 × [(DIH) intramitochondrial reduced diphospyridine nucleotide];  
 
 reaction 16 [(DIH) intramitochondrial reduced diphospyridine nucleotide] + 3.0 × [(XI) low energy intermediate in oxidative phosphorylation] + [(OXY) oxygen] → 3.0 × [(XSI) high energy intermediate in oxidative phosphorylation] + [(DIN) intramitochondrial diphospyridine nucleotide];  
 
 reaction 17 [(XSI) high energy intermediate in oxidative phosphorylation] + [(PID) inorganic phosphate] → [(XSP) phosphorylated intermediate in oxidative phosphorylation];  
 
 reaction 18 [(XSP) phosphorylated intermediate in oxidative phosphorylation] + [(ADP) adenosine diphosphate] → [(TP2) adenosine triphosphate in store 2 (mitochondria)] + [(XI) low energy intermediate in oxidative phosphorylation];  
 
 reaction 19 [(XSI) high energy intermediate in oxidative phosphorylation] → [(XI) low energy intermediate in oxidative phosphorylation];   {(DBP) dibromophenol}
 
 reaction 20 [(TP2) adenosine triphosphate in store 2 (mitochondria)] → [(TP1) adenosine triphosphate in store 1 (cytoplasm)];   {(DBP) dibromophenol}
 
 reaction 21 [(TP1) adenosine triphosphate in store 1 (cytoplasm)] + [(PUE) enzyme concerned in ATP utilization] → [(PPP) enzyme intermediate concerned in ATP utilization];  
 
 reaction 22 [(PPP) enzyme intermediate concerned in ATP utilization] → [(ADP) adenosine diphosphate] + [(PUE) enzyme concerned in ATP utilization] + [(PID) inorganic phosphate];  
 
Rules (32)
 
 Assignment Rule (name: GLU_0) relative GLU = GLU/0.003
 
 Assignment Rule (name: ENZ_0) relative ENZ = ENZ/1.02E-5
 
 Assignment Rule (name: ENG_0) relative ENG = ENG/1.02E-5
 
 Assignment Rule (name: TP1_0) relative TP1 = TP1/0.0015
 
 Assignment Rule (name: ADP_0) relative ADP = ADP/0.001
 
 Assignment Rule (name: GLP_0) relative GLP = GLP/0.001
 
 Assignment Rule (name: ETZ_0) relative ETZ = ETZ/1E-5
 
 Assignment Rule (name: ETG_0) relative ETG = ETG/1E-5
 
 Assignment Rule (name: GPP_0) relative GPP = GPP/0.001
 
 Assignment Rule (name: GAP_0) relative GAP = GAP/0.0002
 
 Assignment Rule (name: DHA_0) relative DHA = DHA/0.0013
 
 Assignment Rule (name: DPN_0) relative DPN = DPN/0.00025
 
 Assignment Rule (name: DPH_0) relative DPH = DPH/0.0002
 
 Assignment Rule (name: PID_0) relative PID = PID/0.005
 
 Assignment Rule (name: DGA_0) relative DGA = DGA/0.0002
 
 Assignment Rule (name: PGA_0) relative PGA = PGA/0.0002
 
 Assignment Rule (name: PYR_0) relative PYR = PYR/0.002
 
 Assignment Rule (name: LAC_0) relative LAC = LAC/0.0012
 
 Assignment Rule (name: DIN_0) relative DIN = DIN/7E-5
 
 Assignment Rule (name: DIH_0) relative DIH = DIH/7E-5
 
 Assignment Rule (name: XI_0) relative XI = XI/6E-5
 
 Assignment Rule (name: XSI_0) relative XSI = XSI/6E-5
 
 Assignment Rule (name: OXY_0) relative OXY = OXY/0.0005
 
 Assignment Rule (name: XSP_0) relative XSP = XSP/6E-5
 
 Assignment Rule (name: TP2_0) relative TP2 = TP2/0.0015
 
 Assignment Rule (name: DBP_0) relative DBP = DBP/0.025
 
 Assignment Rule (name: PUE_0) relative PUE = PUE/3.06E-6
 
 Assignment Rule (name: PPP_0) relative PPP = PPP/3.06
 
 Assignment Rule (name: AGP_0) relative AGP = AGP/0.0013
 
 Assignment Rule (name: MOD_0) relative MOD = MOD/5E-5
 
 Assignment Rule (name: MOB_0) relative MOB = MOB/0.0001
 
 Assignment Rule (name: MOX_0) relative MOX = MOX/5E-5
 
Events (2)
 
 addition of glucose
(GLU) glucose = 0.003
 
 addition of uncoupling agent
(DBP) dibromophenol = 0.025
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 (GLU) glucose
Compartment: cell
Initial concentration: 0.0
 
 (ENZ) hexokinase
Compartment: cell
Initial concentration: 1.0E-5
 
 (ENG) hexokinase-glucose intermediate
Compartment: cell
Initial concentration: 0.0
 
 (TP1) adenosine triphosphate in store 1 (cytoplasm)
Compartment: cell
Initial concentration: 5.0E-4
 
 (ADP) adenosine diphosphate
Compartment: cell
Initial concentration: 1.0E-4
 
 (GLP) glucose 6-phosphate
Compartment: cell
Initial concentration: 0.0
 
 (ETZ) phosphofructokinase
Compartment: cell
Initial concentration: 1.0E-5
 
 (ETG) phosphofructokinase intermediate
Compartment: cell
Initial concentration: 0.0
 
 (GPP) hexose diphosphate
Compartment: cell
Initial concentration: 0.0
 
 (GAP) glyceraldehyde 3-phosphate
Compartment: cell
Initial concentration: 0.0
 
 (DHA) dihydroxacetone phosphate
Compartment: cell
Initial concentration: 0.0
 
 (DPN) extramitochondrial diphospyridine nucleotide
Compartment: cell
Initial concentration: 1.0E-4
 
 (DPH) extramitochondrial reduced diphospyridine nucleotide
Compartment: cell
Initial concentration: 1.0E-4
 
 (PID) inorganic phosphate
Compartment: cell
Initial concentration: 0.0040
 
 (DGA) 1,3 diphosphoglycerate
Compartment: cell
Initial concentration: 0.0
 
 (PGA) 3 phosphoglycerate
Compartment: cell
Initial concentration: 0.0
 
 (PYR) pyruvate
Compartment: cell
Initial concentration: 0.0010
 
 (LAC) lactate
Compartment: cell
Initial concentration: 0.0010
 
 (DIN) intramitochondrial diphospyridine nucleotide
Compartment: cell
Initial concentration: 3.0E-5
 
 (DIH) intramitochondrial reduced diphospyridine nucleotide
Compartment: cell
Initial concentration: 3.0E-5
 
 (XI) low energy intermediate in oxidative phosphorylation
Compartment: cell
Initial concentration: 2.0E-5
 
 (XSI) high energy intermediate in oxidative phosphorylation
Compartment: cell
Initial concentration: 2.0E-5
 
 (OXY) oxygen
Compartment: cell
Initial concentration: 5.0E-4
 
 (XSP) phosphorylated intermediate in oxidative phosphorylation
Compartment: cell
Initial concentration: 2.0E-5
 
 (TP2) adenosine triphosphate in store 2 (mitochondria)
Compartment: cell
Initial concentration: 5.0E-4
 
 (DBP) dibromophenol
Compartment: cell
Initial concentration: 0.0
 
 (PUE) enzyme concerned in ATP utilization
Compartment: cell
Initial concentration: 2.0E-6
 
 (PPP) enzyme intermediate concerned in ATP utilization
Compartment: cell
Initial concentration: 1.0E-6
 
 (AGP) alpha-glycerophosphate
Compartment: cell
Initial concentration: 0.0
 
 (MOD) glyceraldehyde 3-phoshphate dehydrogenase-DPN complex
Compartment: cell
Initial concentration: 5.0E-5
 
 (MOB) acyl enzyme intermediate of glyceraldehyde 3-phoshphate dehydrogenase
Compartment: cell
Initial concentration: 0.0
 
 (MOX) glyceraldehyde 3-phoshphate dehydrogenase
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (32)
 
   relative GLU
Value: NaN   (Units: dimensionless)
 
   relative ENZ
Value: NaN   (Units: dimensionless)
 
   relative ENG
Value: NaN   (Units: dimensionless)
 
   relative TP1
Value: NaN   (Units: dimensionless)
 
   relative ADP
Value: NaN   (Units: dimensionless)
 
   relative GLP
Value: NaN   (Units: dimensionless)
 
   relative ETZ
Value: NaN   (Units: dimensionless)
 
   relative ETG
Value: NaN   (Units: dimensionless)
 
   relative GPP
Value: NaN   (Units: dimensionless)
 
   relative GAP
Value: NaN   (Units: dimensionless)
 
   relative DHA
Value: NaN   (Units: dimensionless)
 
   relative DPN
Value: NaN   (Units: dimensionless)
 
   relative DPH
Value: NaN   (Units: dimensionless)
 
   relative PID
Value: NaN   (Units: dimensionless)
 
   relative DGA
Value: NaN   (Units: dimensionless)
 
   relative PGA
Value: NaN   (Units: dimensionless)
 
   relative PYR
Value: NaN   (Units: dimensionless)
 
   relative LAC
Value: NaN   (Units: dimensionless)
 
   relative DIN
Value: NaN   (Units: dimensionless)
 
   relative DIH
Value: NaN   (Units: dimensionless)
 
   relative XI
Value: NaN   (Units: dimensionless)
 
   relative XSI
Value: NaN   (Units: dimensionless)
 
   relative OXY
Value: NaN   (Units: dimensionless)
 
   relative XSP
Value: NaN   (Units: dimensionless)
 
   relative TP2
Value: NaN   (Units: dimensionless)
 
   relative DBP
Value: NaN   (Units: dimensionless)
 
   relative PUE
Value: NaN   (Units: dimensionless)
 
   relative PPP
Value: NaN   (Units: dimensionless)
 
   relative AGP
Value: NaN   (Units: dimensionless)
 
   relative MOD
Value: NaN   (Units: dimensionless)
 
   relative MOB
Value: NaN   (Units: dimensionless)
 
   relative MOX
Value: NaN   (Units: dimensionless)
 
reaction 1 (1)
 
   k
Value: 3.0E9   (Units: per molar per second)
Constant
 
reaction 2 (1)
 
   k
Value: 1.0E10   (Units: per molar per second)
Constant
 
reaction 3 (1)
 
   k
Value: 4.0E10   (Units: per molar per second)
Constant
 
reaction 4 (1)
 
   k
Value: 4.0E10   (Units: per molar per second)
Constant
 
reaction 5 (1)
 
   k
Value: 100000.0   (Units: per second)
Constant
 
reaction 6 (1)
 
   k
Value: 2.0E9   (Units: per molar per second)
Constant
 
reaction 7 (1)
 
   k
Value: 8.0E7   (Units: per molar per second)
Constant
 
reaction 8 (1)
 
   k
Value: 6.0E11   (Units: per molar per second)
Constant
 
reaction 9 (1)
 
   k
Value: 4.0E8   (Units: per molar per second)
Constant
 
reaction 10 (1)
 
   k
Value: 6.0E9   (Units: per molar per second)
Constant
 
reaction 11 (1)
 
   k
Value: 1.0E10   (Units: per molar per second)
Constant
 
reaction 12 (1)
 
   k
Value: 5.0E9   (Units: per molar per second)
Constant
 
reaction 13 (1)
 
   k
Value: 5.0E8   (Units: per molar per second)
Constant
 
reaction 14 (1)
 
   k
Value: 1.0E7   (Units: per molar per second)
Constant
 
reaction 15 (1)
 
   k
Value: 2.0E7   (Units: per molar per second)
Constant
 
reaction 16 (1)
 
   k
Value: 7.5E12   (Units: per molar squared per second)
Constant
 
reaction 17 (1)
 
   k
Value: 4.0E8   (Units: per molar per second)
Constant
 
reaction 18 (1)
 
   k
Value: 1.5E10   (Units: per molar per second)
Constant
 
reaction 19 (1)
 
   k
Value: 1.2E8   (Units: per molar per second)
Constant
 
reaction 20 (1)
 
   k
Value: 4000000.0   (Units: per molar per second)
Constant
 
reaction 21 (1)
 
   k
Value: 3.0E9   (Units: per molar per second)
Constant
 
reaction 22 (1)
 
   k
Value: 2000000.0   (Units: per second)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000281

Curator's comment: (updated: 24 Nov 2010 20:58:31 GMT)

Reproduction of figure 3/Graph1 from the original publication. The time course simulation was performed using Copasi 4.6.

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