MODEL1202170000
type: SBMLModel
time units: 291235
volume units: 291259
reaction: 292951
units def: 291211
parameter: 291465
species: meta s2 e1
rule: 291723
rule: 291552
species: meta a3 e5
notes: This model is from the article: An old paper revisited: ‘‘A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load’’ by V.V. Dynnik, R. Heinrich and E.E. Sel’kov Nazaret C, Mazat JP. J Theor Biol 2008 Jun;252(3):520-9. 18304584 , Abstract: We revisit an old Russian paper by V.V. Dynnik, R. Heinrich and E.E. Sel’kov (1980a, b) describing: ‘‘A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load’’. We analyse the model mathematically and calculate the control coefficients as a function of ATPase loads. We also evaluate the structure of the metabolic network in terms of elementary flux modes. We show how this model can respond to an ATPase load as well as to the glucose supply. We also show how this simple model can help in understanding the articulation between the major blocks of energetic metabolism, i.e. glycolysis, the Krebs cycle and the H-transporting shuttles. Note: "dynnik_v1.xml": created directly from "heinrich.sci" model file provided by Christine Nazaret IDs changed to as per the paper initial conditions set to steady state results of Fig. 3 may be reproduced by running a a parameter scan over b15 in COPASI "dynnik_v2.xml": rescaled species such as s2_e1 = s2 * e1 are introduced whose evolution may be described through reaction participation, rather than via ODEs original variables are retained as global parameters To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restr…
species: meta r2
species: meta r1 e6
species: meta a2
parameter: 291307
reaction: 292190
reaction: 291735
reaction: 292055
parameter: 291295
parameter: 291380
parameter: 291332
units def: 291259
parameter: 291417
reaction: 293063
reaction: 292878
rule: 291686
parameter: 291490
parameter: 291356
rule: 291625
is described by: http://identifiers.org/pubmed/18304584
reaction: 292734
species: meta n1
reaction: 292650
is: http://identifiers.org/taxonomy/9606
species: meta a1 e5
area units: area
curated: false
reaction: 292103
rule: 291649
parameter: 291528
compartment: 291283
species: meta s5 e4
reaction: 292566
species: meta i1 e8
parameter: 291368
species: meta i3
parameter: 291453
parameter: 291405
rule: 291661
species: meta i2 e8
substance units: 291211
rule: 291577
reaction: 292372
parameter: 291477
species: meta s3 e2
reaction: 291859
parameter: 291503
reaction: 292470
reaction: 293123
rule: 291601
reaction: 291956
units def: 291235
rule: 291540
rule: 291711
parameter: 291344
reaction: 292830
rule: 291637
parameter: 291441
parameter: 291319
name: Nazaret2008_Dynnik1980_CarbohydrateEnergyMetabolism
rule: 291564
parameter: 291392
reaction: 292782
parameter: 291429
length unit: length
species: meta s4 e3
species: meta s1
reaction: 292287
rule: 291589
species: meta c1

291247
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS

291271
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS

292951
type: Reaction
kinetic law: 293012
notes: oxidative phosphorylation
is: SBO:0000176
reactant: 292976
name: v16
reversible: true
product: 292988
reactant: 292963
fast: false
product: 293000

293051
type: LocalParameter
units: dimensionless
value: 0.1

293038
type: LocalParameter
units: dimensionless
value: 0.1

293025
type: LocalParameter
units: dimensionless
value: 5.0

292976
type: SpeciesReference
stoichiometry: 3.0
species: meta a2

meta a2
type: Species
has only substance units: false
initial amount: NaN
is: C00008
name: ADP
in compartment: 291283
initial concentration: 0.1
is: SBO:0000247
is: CHEBI:456216
constant: false
boundary condition: true

291283
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0

292988
type: SpeciesReference
stoichiometry: 3.0
species: meta a3 e5

meta a3 e5
type: Species
name: ATP
boundary condition: false
is: C00002
is: CHEBI:30616
in compartment: 291283
has only substance units: false
is: SBO:0000247
initial amount: NaN
constant: false
initial concentration: 3.2

292963
type: SpeciesReference
stoichiometry: 1.0
species: meta n2 e7

meta n2 e7
type: Species
initial amount: NaN
boundary condition: false
is: SBO:0000247
is: C00004
has only substance units: false
in compartment: 291283
is: CHEBI:57945
name: NADHm
constant: false
initial concentration: 0.002

293000
type: SpeciesReference
stoichiometry: 1.0
species: meta n1

meta n1
type: Species
constant: false
boundary condition: true
is: CHEBI:57540
initial concentration: 0.99
has only substance units: false
name: NADm
is: C00003
in compartment: 291283
is: SBO:0000247
initial amount: NaN

291223
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS

291465
type: Parameter
constant: false
units: dimensionless
value: NaN
name: AMP

meta s2 e1
type: Species
is: SBO:0000247
name: aGP
constant: false
has only substance units: false
is: C00093
in compartment: 291283
initial amount: NaN
boundary condition: false
initial concentration: 0.5
is: CHEBI:57597

meta r2
type: Species
in compartment: 291283
is: SBO:0000247
is: C00004
initial amount: NaN
constant: false
initial concentration: 0.5
name: NADHc
boundary condition: true
is: CHEBI:57945
has only substance units: false

meta r1 e6
type: Species
is: C00003
initial amount: NaN
boundary condition: false
initial concentration: 0.1
constant: false
is: CHEBI:57540
name: NADc
is: SBO:0000247
in compartment: 291283
has only substance units: false

291307
type: Parameter
constant: true
units: dimensionless
value: 1.0

292190
type: Reaction
reactant: 292214
reactant: 292202
notes: glycolytic reaction
product: 292239
reversible: true
fast: false
name: v6
product: 292226
kinetic law: 292251
is: SBO:0000176

292214
type: SpeciesReference
stoichiometry: 1.0
species: meta r2

292202
type: SpeciesReference
stoichiometry: 1.0
species: meta s4 e3

meta s4 e3
type: Species
initial amount: NaN
name: Pyr
boundary condition: false
in compartment: 291283
has only substance units: false
constant: false
initial concentration: 0.01
is: C00022
is: SBO:0000247
is: CHEBI:15361

292239
type: SpeciesReference
stoichiometry: 1.0
species: meta r1 e6

292226
type: SpeciesReference
stoichiometry: 1.0
species: meta s5 e4

meta s5 e4
type: Species
boundary condition: false
is: C00186
is: CHEBI:16651
name: Lac
initial concentration: 0.01
has only substance units: false
initial amount: NaN
is: SBO:0000247
constant: false
in compartment: 291283

292275
type: LocalParameter
units: dimensionless
value: 0.003

292263
type: LocalParameter
units: dimensionless
value: 200.0

291735
type: Reaction
notes: glycolytic reaction
product: 291772
product: 291760
modifier: 291784
reversible: true
name: v1
is: SBO:0000176
reactant: 291747
kinetic law: 291796
fast: false

291772
type: SpeciesReference
stoichiometry: 2.0
species: meta a2

291760
type: SpeciesReference
stoichiometry: 2.0
species: meta s1

meta s1
type: Species
in compartment: 291283
name: GAP
is: CHEBI:58027
is: C00661
has only substance units: false
initial concentration: 0.1
constant: false
boundary condition: false
initial amount: NaN
is: SBO:0000247

meta a1 e5
type: Species
constant: false
initial amount: NaN
boundary condition: false
in compartment: 291283
is: SBO:0000247
is: C00020
initial concentration: 0.4
is: CHEBI:456215
has only substance units: false
name: AMP

291747
type: SpeciesReference
stoichiometry: 2.0
species: meta a3 e5

291847
type: LocalParameter
units: dimensionless
value: 0.1

291834
type: LocalParameter
units: dimensionless
value: 0.1

291822
type: LocalParameter
units: dimensionless
value: 0.003

291809
type: LocalParameter
units: dimensionless
value: 1.0

292055
type: Reaction
kinetic law: 292079
reactant: 292067
notes: glycolytic intermediate efflux
is: SBO:0000176
fast: false
reversible: true
name: v4

292091
type: LocalParameter
units: dimensionless
value: 0.01

292067
type: SpeciesReference
stoichiometry: 1.0
species: meta s3 e2

meta s3 e2
type: Species
boundary condition: false
in compartment: 291283
constant: false
is: C00236
initial amount: NaN
name: 13DPG
is: SBO:0000247
has only substance units: false
is: CHEBI:57604
initial concentration: 0.5

291295
type: Parameter
constant: true
units: dimensionless
value: 1.0

291380
type: Parameter
constant: true
units: dimensionless
value: 0.2

291332
type: Parameter
constant: true
units: dimensionless
value: 1.0

291417
type: Parameter
constant: false
units: dimensionless
value: NaN
name: 13DPG

293063
type: Reaction
kinetic law: 293099
product: 293087
reactant: 293075
notes: NADH dehydrogenase
is: SBO:0000176
fast: false
reversible: true
name: v17

293111
type: LocalParameter
units: dimensionless
value: 0.01

293087
type: SpeciesReference
stoichiometry: 1.0
species: meta n2 e7

293075
type: SpeciesReference
stoichiometry: 1.0
species: meta n1

292878
type: Reaction
kinetic law: 292914
product: 292902
reactant: 292890
notes: total ATPase reaction
is: SBO:0000176
fast: false
reversible: true
name: v15

292938
type: LocalParameter
units: dimensionless
value: 0.1

292926
type: LocalParameter
units: dimensionless
value: 1.0

292902
type: SpeciesReference
stoichiometry: 1.0
species: meta a2

292890
type: SpeciesReference
stoichiometry: 1.0
species: meta a3 e5

291490
type: Parameter
constant: false
units: dimensionless
value: NaN
name: NADHm

291356
type: Parameter
constant: true
units: dimensionless
value: 0.2

292734
type: Reaction
kinetic law: 292758
reactant: 292746
notes: glycolytic intermediate efflux
is: SBO:0000176
fast: false
reversible: true
name: v12

292770
type: LocalParameter
units: dimensionless
value: 0.1

292746
type: SpeciesReference
stoichiometry: 1.0
species: meta s4 e3

292650
type: Reaction
name: v11
reversible: true
product: 292698
is: SBO:0000176
product: 292686
kinetic law: 292710
fast: false
reactant: 292674
reactant: 292662
notes: Krebs cycle

292698
type: SpeciesReference
stoichiometry: 1.0
species: meta i2 e8

meta i2 e8
type: Species
initial concentration: 0.01
boundary condition: false
is: C00149
name: Mal
is: SBO:0000247
initial amount: NaN
in compartment: 291283
has only substance units: false
is: CHEBI:15589
constant: false

292686
type: SpeciesReference
stoichiometry: 3.0
species: meta n2 e7

292722
type: LocalParameter
units: dimensionless
value: 3.0

292674
type: SpeciesReference
stoichiometry: 3.0
species: meta n1

292662
type: SpeciesReference
stoichiometry: 1.0
species: meta i3

meta i3
type: Species
initial concentration: 0.9
is: C00158
boundary condition: true
is: SBO:0000247
has only substance units: false
constant: false
is: CHEBI:16947
initial amount: NaN
in compartment: 291283
name: Cit

292103
type: Reaction
product: 292152
product: 292140
notes: glycolytic reaction
reversible: true
name: v5
reactant: 292115
kinetic law: 292165
is: SBO:0000176
fast: false
reactant: 292127

292152
type: SpeciesReference
stoichiometry: 2.0
species: meta a3 e5

292140
type: SpeciesReference
stoichiometry: 1.0
species: meta s4 e3

292115
type: SpeciesReference
stoichiometry: 1.0
species: meta s3 e2

292178
type: LocalParameter
units: dimensionless
value: 10.0

292127
type: SpeciesReference
stoichiometry: 2.0
species: meta a2

291528
type: Parameter
constant: false
units: dimensionless
value: NaN
name: CoASAc

292566
type: Reaction
reversible: true
reactant: 292578
is: SBO:0000176
fast: false
reactant: 292590
kinetic law: 292626
name: v10
notes: Krebs cycle
product: 292602
product: 292614

292578
type: SpeciesReference
stoichiometry: 1.0
species: meta i1 e8

meta i1 e8
type: Species
initial amount: NaN
in compartment: 291283
initial concentration: 0.01
is: CHEBI:16452
name: Oxa
constant: false
boundary condition: false
has only substance units: false
is: SBO:0000247
is: C00036

292590
type: SpeciesReference
stoichiometry: 1.0
species: meta c2 e9

meta c2 e9
type: Species
name: CoASAc
initial amount: NaN
boundary condition: false
is: CHEBI:57288
is: C00024
initial concentration: 0.01
has only substance units: false
constant: false
is: SBO:0000247
in compartment: 291283

292638
type: LocalParameter
units: dimensionless
value: 5.0

292602
type: SpeciesReference
stoichiometry: 1.0
species: meta i3

292614
type: SpeciesReference
stoichiometry: 1.0
species: meta c1

meta c1
type: Species
name: CoA
in compartment: 291283
is: SBO:0000247
has only substance units: false
is: CHEBI:57287
boundary condition: true
is: C00010
initial amount: NaN
initial concentration: 0.95
constant: false

291368
type: Parameter
constant: true
units: dimensionless
value: 0.2

291453
type: Parameter
constant: false
units: dimensionless
value: NaN
name: ATP

291405
type: Parameter
constant: false
units: dimensionless
value: NaN
name: aGP

292372
type: Reaction
reactant: 292396
fast: false
reversible: true
product: 292433
notes: pyruvate dehydrogenase
reactant: 292409
kinetic law: 292446
is: SBO:0000176
name: v8
reactant: 292384
product: 292421

292396
type: SpeciesReference
stoichiometry: 1.0
species: meta c1

292433
type: SpeciesReference
stoichiometry: 1.0
species: meta c2 e9

292409
type: SpeciesReference
stoichiometry: 1.0
species: meta n1

292458
type: LocalParameter
units: dimensionless
value: 3.0

292384
type: SpeciesReference
stoichiometry: 1.0
species: meta s4 e3

292421
type: SpeciesReference
stoichiometry: 1.0
species: meta n2 e7

291477
type: Parameter
constant: false
units: dimensionless
value: NaN
name: NADc

291859
type: Reaction
notes: cytoplasmic alpha-glycerophosphate reaction of H-transporter
product: 291908
is: SBO:0000176
reversible: true
name: v2
kinetic law: 291920
product: 291895
reactant: 291883
reactant: 291871
fast: false

291908
type: SpeciesReference
stoichiometry: 1.0
species: meta r1 e6

291944
type: LocalParameter
units: dimensionless
value: 0.1

291932
type: LocalParameter
units: dimensionless
value: 20.0

291895
type: SpeciesReference
stoichiometry: 1.0
species: meta s2 e1

291883
type: SpeciesReference
stoichiometry: 1.0
species: meta r2

291871
type: SpeciesReference
stoichiometry: 1.0
species: meta s1

291503
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Oxa

292470
type: Reaction
fast: false
reactant: 292494
reactant: 292482
name: v9
product: 292518
reversible: true
product: 292506
is: SBO:0000176
kinetic law: 292530
notes: Krebs cycle

292494
type: SpeciesReference
stoichiometry: 1.0
species: meta n1

292482
type: SpeciesReference
stoichiometry: 1.0
species: meta i2 e8

292518
type: SpeciesReference
stoichiometry: 1.0
species: meta i1 e8

292506
type: SpeciesReference
stoichiometry: 1.0
species: meta n2 e7

292554
type: LocalParameter
units: dimensionless
value: 25.0

292542
type: LocalParameter
units: dimensionless
value: 100.0

293123
type: Reaction
reactant: 293147
product: 293159
notes: adenylate kinase
is: SBO:0000176
fast: false
kinetic law: 293172
reversible: true
name: v18
reactant: 293135

293147
type: SpeciesReference
stoichiometry: 1.0
species: meta a1 e5

293159
type: SpeciesReference
stoichiometry: 2.0
species: meta a2

293196
type: LocalParameter
units: dimensionless
value: 1.0

293184
type: LocalParameter
units: dimensionless
value: 100.0

293135
type: SpeciesReference
stoichiometry: 1.0
species: meta a3 e5

291956
type: Reaction
notes: glycolytic reaction
is: SBO:0000176
product: 291994
reactant: 291969
kinetic law: 292018
fast: false
reversible: true
reactant: 291981
product: 292006
name: v3

291994
type: SpeciesReference
stoichiometry: 1.0
species: meta s3 e2

291969
type: SpeciesReference
stoichiometry: 1.0
species: meta s1

292042
type: LocalParameter
units: dimensionless
value: 25.0

292030
type: LocalParameter
units: dimensionless
value: 10.0

291981
type: SpeciesReference
stoichiometry: 1.0
species: meta r1 e6

292006
type: SpeciesReference
stoichiometry: 1.0
species: meta r2

291344
type: Parameter
constant: true
units: dimensionless
value: 4.0

292830
type: Reaction
kinetic law: 292854
reactant: 292842
notes: alpha-glycerophosphate efflux
is: SBO:0000176
fast: false
reversible: true
name: v14

292866
type: LocalParameter
units: dimensionless
value: 0.5

292842
type: SpeciesReference
stoichiometry: 1.0
species: meta s2 e1

291441
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Lac

291319
type: Parameter
constant: true
units: dimensionless
value: 1.0

291392
type: Parameter
constant: true
units: dimensionless
value: 0.2

292782
type: Reaction
kinetic law: 292806
reactant: 292794
notes: glycolytic intermediate efflux
is: SBO:0000176
fast: false
reversible: true
name: v13

292818
type: LocalParameter
units: dimensionless
value: 0.1

292794
type: SpeciesReference
stoichiometry: 1.0
species: meta s5 e4

291429
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Pyr

292287
type: Reaction
kinetic law: 292348
reversible: true
reactant: 292299
fast: false
product: 292324
is: SBO:0000176
product: 292336
notes: mitochondrial alpha-glycerophosphate reaction of H-transporter
name: v7
reactant: 292312

292360
type: LocalParameter
units: dimensionless
value: 25.0

292299
type: SpeciesReference
stoichiometry: 1.0
species: meta s2 e1

292324
type: SpeciesReference
stoichiometry: 1.0
species: meta s1

292336
type: SpeciesReference
stoichiometry: 1.0
species: meta n2 e7

292312
type: SpeciesReference
stoichiometry: 1.0
species: meta n1

291516
type: Parameter
constant: false
units: dimensionless
value: NaN
name: Mal

ORG:
  orgname: University of Manchester
n:
  given: Kieran
  family: Smallbone

W3 CDTF: Fri May 11 14:05:24 BST 2012

ORG:
  orgname: Inistitut Polytechnique Bordeaux
n:
  given: Christine
  family: Nazaret

ORG:
  orgname: University of Manchester
n:
  given: Kieran
  family: Smallbone

ORG:
  orgname: Inistitut Polytechnique Bordeaux
n:
  given: Christine
  family: Nazaret

W3 CDTF: Fri Feb 17 11:04:55 GMT 2012

W3 CDTF: Wed Feb 15 00:00:00 GMT 2012

ORG:
  orgname: University of Manchester
n:
  given: Kieran
  family: Smallbone

ORG:
  orgname: Inistitut Polytechnique Bordeaux
n:
  given: Christine
  family: Nazaret

W3 CDTF: Fri May 11 14:05:24 BST 2012