BIOMD0000000108
type: SBMLModel
reaction: metaid_0000037
species: metaid_0000054
parameter: metaid_0000057
reaction: metaid_0000045
length unit: length
is version of: GO:0004784
reaction: metaid_0000060
parameter: metaid_0000030
parameter: metaid_0000032
parameter: metaid_0000025
reaction: metaid_0000040
parameter: metaid_0000020
curated: true
reaction: metaid_0000048
notes: This model is according to the paper from Axel Kowald Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase. Reactions from 1 to 17 are listed in the paper, note that for clarity species whose concentrations are assumed to be constant (e.g.water, oxygen,protons, metal ions) are omitted from the diagram. In the paper, v16 is a fast reaction, but we do not use fast reaction in the model. Figure2 has been reproduced by both SBMLodeSolver and Copasi4.0.20(development) . Figure 3 has been obtained with Copasi4.0.20(development) using parameter scan. The steady-state of [LOO*] a little bit lower than showed on the paper, I guess it may be the simulation method used in the paper use fast reaction and also the reaction (5) listed on Page 831 on the paper is slightly different from equation (2) on Page 832. The rest of them are the quite the same. 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 restricted way or not. 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.
occurs in: http://identifiers.org/taxonomy/131567
parameter: metaid_0000017
reaction: metaid_0000043
rule: metaid_0000055
area units: metaid_0000005
parameter: metaid_0000029
reaction: metaid_0000051
species: metaid_0000012
is: MODEL5128825728
parameter: metaid_0000031
parameter: metaid_0000024
reaction: metaid_0000039
volume units: metaid_0000004
parameter: metaid_0000059
reaction: metaid_0000047
species: metaid_0000010
modified:
  W3 CDTF: Thu Jul 05 15:40:13 BST 2012
creator:
  ORG:
    orgname: BNMC
  n:
    given: Enuo
    family: He
parameter: metaid_0000027
species: metaid_0000009
reaction: metaid_0000042
is described by: http://identifiers.org/pubmed/16085106
parameter: metaid_0000022
compartment: metaid_0000003
parameter: metaid_0000028
parameter: metaid_0000019
species: metaid_0000011
species: metaid_0000004
substance units: metaid_0000084
species: metaid_0000005
reaction: metaid_0000050
parameter: metaid_0000023
reaction: metaid_0000038
reaction: metaid_0000046
reaction: metaid_0000033
species: metaid_0000014
name: Kowald2006_SOD
parameter: metaid_0000026
reaction: metaid_0000041
time units: metaid_0000086
is version of: GO:0006801
parameter: metaid_0000021
reaction: metaid_0000049
parameter: metaid_0000018
reaction: metaid_0000044
created:
  W3 CDTF: Wed Mar 28 13:43:05 BST 2007
rule: metaid_0000056
species: metaid_0000053

metaid_0000037
type: Reaction
kinetic law: 605159
reactant: 605146
reactant: 605133
is part of: GO:0004784
fast: false
reversible: false
name: v2

605146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

metaid_0000005
type: Species
is version of: IPR001424
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-6
initial amount: NaN
in compartment: metaid_0000003
name: Cu(II)ZnSOD

metaid_0000003
type: Compartment
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

605133
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000004
type: Species
initial amount: NaN
boundary condition: false
has only substance units: false
constant: false
is: CHEBI:18421
is: C00704
initial concentration: 0.0
name: O2*-
in compartment: metaid_0000003

metaid_0000054
type: Species
has version: IPR002226
constant: true
boundary condition: false
has only substance units: false
initial concentration: 1.0E-5
initial amount: NaN
in compartment: metaid_0000003
name: Cat

metaid_0000057
type: Parameter
constant: false
value: 0.0
name: HO2*

metaid_0000045
type: Reaction
kinetic law: 605493
product: 605481
reactant: 605469
fast: false
reversible: false
name: v11

605481
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000014
type: Species
is version of: CHEBI:18059
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: L*

605469
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000011
type: Species
is: CHEBI:29191
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: HO*

metaid_0000060
type: Reaction
kinetic law: 605698
reactant: 605686
notes: Reaction16 showed in the paper is a fast equilibrium reaction. HO2* =" H+" + "O2*-". So in the equation (1) in the paper, you will see there is one item k10*"HO2*" . However, most simulation software does not support fast reaction yet, so curator creat this fake v16 reaction in order to make the final ODE correct.
fast: false
reversible: true
name: v16

605686
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000030
type: Parameter
constant: true
value: 30000.0
name: k17

metaid_0000032
type: Parameter
constant: true
value: 88000.0
name: k19

metaid_0000025
type: Parameter
constant: true
value: 1000.0
name: k10

metaid_0000040
type: Reaction
kinetic law: 605313
product: 605301
reactant: 605289
reactant: 605276
fast: false
reversible: false
name: v5

605301
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000011

605289
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000009
type: Species
initial concentration: 0.0
constant: false
in compartment: metaid_0000003
is: C00027
boundary condition: false
is: CHEBI:16240
initial amount: NaN
name: H2O2
has only substance units: false

605276
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000020
type: Parameter
constant: true
value: 100000.0
name: k4

metaid_0000048
type: Reaction
kinetic law: 605565
reactant: 605553
is version of: GO:0009055
fast: false
reversible: false
name: v13b

605553
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

metaid_0000017
type: Parameter
constant: true
value: 6.6E-7
name: k1

metaid_0000043
type: Reaction
kinetic law: 605421
reactant: 605409
is version of: GO:0044248
fast: false
reversible: false
name: v9

605409
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000055
notes: HO2*=O2*/100

metaid_0000029
type: Parameter
constant: true
value: 0.0087
name: k13b

metaid_0000051
type: Reaction
kinetic law: 605674
reactant: 605662
fast: false
reversible: false
name: v19

605662
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000010

metaid_0000010
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: LOO*

metaid_0000012
type: Species
is: C01025
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: LOOH

metaid_0000031
type: Parameter
constant: true
value: 7.0
name: k18

metaid_0000024
type: Parameter
constant: true
value: 1000000.0
name: k9

metaid_0000039
type: Reaction
kinetic law: 605263
product: 605250
reactant: 605237
reactant: 605224
fast: false
reversible: false
name: v4

605250
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

605237
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

605224
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000059
type: Parameter
constant: false
value: 0.0
name: Cu(I)ZnSOD

metaid_0000047
type: Reaction
kinetic law: 605541
product: 605529
is version of: GO:0009055
fast: false
reversible: false
name: v13a

605529
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

metaid_0000027
type: Parameter
constant: true
value: 0.38
name: k12

metaid_0000042
type: Reaction
kinetic law: 605397
modifier: 605385
reactant: 605373
is version of: GO:0004096
is version of: http://identifiers.org/ec-code/1.11.1.6
fast: false
reversible: false
name: v7

605373
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000022
type: Parameter
constant: true
value: 1.0
name: k6

metaid_0000028
type: Parameter
constant: true
value: 0.0087
name: k13a

metaid_0000019
type: Parameter
constant: true
value: 1.6E9
name: k3

metaid_0000050
type: Reaction
kinetic law: 605650
product: 605638
product: 605626
reactant: 605614
fast: false
reversible: false
name: v18

605638
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

605626
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

605614
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000023
type: Parameter
constant: true
value: 3.4E7
name: k7

metaid_0000038
type: Reaction
product: 605185
kinetic law: 605211
fast: false
is part of: GO:0004784
reversible: false
product: 605198
is version of: R05743
reactant: 605172
is version of: http://identifiers.org/ec-code/1.15.1.2
name: v3

605185
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

605198
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

605172
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000046
type: Reaction
kinetic law: 605517
reactant: 605505
fast: false
reversible: false
name: v12

605505
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000033
type: Reaction
kinetic law: 605120
product: 605108
is version of: GO:0042554
fast: false
reversible: false
name: v1

605108
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000026
type: Parameter
constant: true
value: 2.5E8
name: k11

metaid_0000041
type: Reaction
kinetic law: 605361
modifier: 605349
product: 605337
reactant: 605325
fast: false
reversible: false
name: v6

605337
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000011

605325
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000021
type: Parameter
constant: true
value: 20000.0
name: k5

metaid_0000049
type: Reaction
kinetic law: 605601
product: 605589
reactant: 605577
fast: false
reversible: false
name: v17

605589
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

605577
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000018
type: Parameter
constant: true
value: 1.6E9
name: k2

metaid_0000044
type: Reaction
kinetic law: 605457
product: 605445
product: 605433
fast: false
reversible: false
name: v10

605445
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

605433
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000056
notes: Cu(I)ZnSOD=SODtotal-Cu(II)ZnSOD

metaid_0000053
type: Species
is version of: IPR001424
constant: true
boundary condition: false
has only substance units: false
initial concentration: 1.0E-5
initial amount: NaN
in compartment: metaid_0000003
name: SODtotal