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BIOMD0000000103
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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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952816
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fast: false
reversible: true
name: Cleaved-Caspase 3 binding with Xiap-Caspase 9
type: Reaction

metaid_0000100
constant: true
value: 0.001
type: Parameter

metaid_0000073
constant: true
value: 0.1
type: Parameter

952660
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

953585
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

953537
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

952454
exponent: -1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000014
is version of: P55211
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000118
name: Caspase 9 cleaved
type: Species

953057
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

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

952528
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

952612
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000027
type: Reaction
name: cleaved Caspase 9 XIAP binding
is version of: GO:0005515
reversible: true
is version of: GO:0006412
product: 953081
fast: false
reactant: 953057
reactant: 953069
kinetic law: 953093

952865
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000111
constant: true
value: 1.0
type: Parameter

metaid_0000064
constant: true
value: 0.002
type: Parameter

952913
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

952792
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

953946
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

953237
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000078
constant: true
value: 0.002
type: Parameter

metaid_0000051
kinetic law: 953693
reactant: 953681
is version of: GO:0044257
fast: false
reversible: false
name: Caspase9_star-Xiap-Caspase3_star degradation
type: Reaction

953996
stoichiometry: 1.0
species: metaid_0000046
type: SpeciesReference

953874
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000036
kinetic law: 953429
reactant: 953417
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1-Caspase 9-Xiap degradation
type: Reaction

953321
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

953705
stoichiometry: 1.0
species: metaid_0000048
type: SpeciesReference

metaid_0000026
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
type: Reaction

metaid_0000090
constant: true
value: 0.001
type: Parameter

metaid_0000112
constant: true
value: 1.0
type: Parameter

952576
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000065
constant: true
value: 0.1
type: Parameter

954164
stoichiometry: 1.0
species: metaid_0000047
type: SpeciesReference

953489
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

954068
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000050
kinetic law: 953669
reactant: 953657
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1-Caspase9-Xiap-Caspase3_star degradation
type: Reaction

metaid_0000079
constant: true
value: 0.1
type: Parameter

952925
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000039
kinetic law: 953501
reactant: 953489
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 3 cleaved degradation
type: Reaction

metaid_0000025
reactant: 952961
fast: false
is: GO:0030693
type: Reaction
name: Caspase 9 cleavage by cleaved caspase 3 when Apaf-1 is bound
reactant: 952949
kinetic law: 952997
product: 952985
is: http://identifiers.org/ec-code/3.4.22.56
product: 952973
reversible: false

953153
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

952853
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

952479
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

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

953069
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

953609
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000011
is version of: P42574
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000118
name: Caspase 3 cleaved
type: Species

metaid_0000066
constant: true
value: 5.0E-6
type: Parameter

metaid_0000076
constant: true
value: 2.0E-4
type: Parameter

metaid_0000024
kinetic law: 952937
is: http://identifiers.org/ec-code/3.4.22.56
reactant: 952901
type: Reaction
reversible: false
product: 952925
product: 952913
reactant: 952889
fast: false
is: GO:0030693
name: Caspase 9 cleavage by cleaved caspase 3

953561
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000038
kinetic law: 953477
product: 953465
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 3 turnover
type: Reaction

metaid_0000110
constant: true
value: 1.0
type: Parameter

953633
stoichiometry: 1.0
species: metaid_0000045
type: SpeciesReference

953984
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

953009
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

952768
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

953886
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000010
is version of: P42574
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: metaid_0000118
name: Caspase 3
type: Species

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

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

given: Harish
family: Dharuri

ORG:
  orgname: California Institute of Technology

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

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

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

orgname: Humboldt University Berlin

given: Stefan
family: Legewie