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type: SBMLModel
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notes: This model represents the non-competitive binding of XIAP to Casapase-3 and Caspase-9. In other words, XIAP mediated feedback is abolished in this model. The authors state that this leads to bistable-reversible behaviour as depicted in Fig 4C. The wild-type model displays a bistable-irreversible profile. This shows that irreversibility requires XIAP mediated feedback. The model was tested on MathSBML. However, please note that the paper does not contain any figure that corresponds to simulation of the Non-Competitive model. 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.
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stoichiometry: 1.0
species: metaid_0000048

954176
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

954164
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

metaid_0000044
type: Reaction
kinetic law: 953621
reactant: 953609
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1 Caspase 9 cleaved-Xiap degradation

953609
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000071
type: Parameter
constant: true
value: 0.001

metaid_0000097
type: Parameter
constant: true
value: 0.001

metaid_0000026
type: Reaction
kinetic law: 953045
product: 953033
reactant: 953021
reactant: 953009
is version of: GO:0005515
fast: false
reversible: true
name: cleaved Caspase 9 Apaf-1 binding

953033
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

953021
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

953009
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000029
type: Reaction
kinetic law: 953189
product: 953177
reactant: 953165
reactant: 953153
is version of: GO:0005515
fast: false
reversible: true
name: cleaved Caspase 9-Xiap Apaf-1 binding

953177
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

953165
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

953153
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

metaid_0000102
type: Parameter
constant: true
value: 0.001

metaid_0000074
type: Parameter
constant: true
value: 0.003

metaid_0000077
type: Parameter
constant: true
value: 2.0E-4

metaid_0000100
type: Parameter
constant: true
value: 0.001

metaid_0000084
type: Parameter
constant: true
value: 0.002

metaid_0000087
type: Parameter
constant: true
value: 0.0035

metaid_0000031
type: Reaction
fast: false
is: http://identifiers.org/ec-code/3.4.22.62
name: Caspase 3 cleavage by cleaved Caspase 9 - Apaf-1
reactant: 953273
is version of: GO:0030693
reversible: false
kinetic law: 953309
product: 953297
product: 953285
reactant: 953261

953273
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

953297
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

953285
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

953261
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000019
type: Reaction
product: 952672
kinetic law: 952684
is: http://identifiers.org/ec-code/3.4.22.62
product: 952660
reactant: 952636
reversible: false
reactant: 952648
name: Caspase 3 cleavage by Caspase 9-Apaf-1
is version of: GO:0006919
fast: false

952672
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

952660
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

952636
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

952648
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000108
type: Parameter
constant: true
value: 0.001

metaid_0000105
type: Parameter
constant: true
value: 0.001

metaid_0000090
type: Parameter
constant: true
value: 0.001

metaid_0000114
type: SBMLUnitsDef
unit: 952442
unit: 952430
unit: 952418
name: nM_per_sec

952442
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

952430
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

952418
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000064
type: Parameter
constant: true
value: 0.002

metaid_0000109
type: Parameter
constant: true
value: 1.0

metaid_0000067
type: Parameter
constant: true
value: 3.5E-4

metaid_0000068
type: Parameter
constant: true
value: 0.001

metaid_0000052
type: Reaction
kinetic law: 953717
reactant: 953705
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1-Caspase9_star-Xiap-Caspase3_star degradation

953705
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

metaid_0000055
type: Reaction
kinetic law: 953862
product: 953850
reactant: 953838
reactant: 953826
is version of: GO:0005515
fast: false
reversible: true
name: Cleaved-Caspase 3 binding with Cleaved-Xiap-Caspase 9

953850
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

953838
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

953826
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000021
type: Reaction
product: 952768
is version of: GO:0005515
kinetic law: 952780
reversible: true
reactant: 952744
is version of: GO:0043027
reactant: 952756
name: Caspase 9-Apaf-1 Xiap binding
fast: false

952768
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

952744
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

952756
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

W3 CDTF: Thu Jul 05 15:46:07 BST 2012

metaid_0000070
type: Parameter
constant: true
value: 0.001

metaid_0000034
type: Reaction
kinetic law: 953381
product: 953369
is version of: GO:0044257
fast: false
reversible: false
name: Xiap turnover

953369
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000060
type: Reaction
kinetic law: 954104
product: 954092
reactant: 954080
reactant: 954068
is version of: GO:0005515
fast: false
reversible: true
name: Binding of cleaved Caspase 9-Apaf-1 to cleaved Caspase 3-Xiap

954092
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

954080
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

954068
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

metaid_0000037
type: Reaction
kinetic law: 953453
reactant: 953441
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1-Caspase 9 degradation

953441
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

ORG:
  orgname: Humboldt Universtity Berlin
n:
  given: Hanspeter
  family: Herzel

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

ORG:
  orgname: Humboldt University Berlin
n:
  given: Nils
  family: Bluethgen

W3 CDTF: Thu Apr 20 11:59:50 BST 2006

ORG:
  orgname: Humboldt University Berlin
n:
  given: Stefan
  family: Legewie