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BIOMD0000000102 - Legewie2006_apoptosis_WT

 

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Reference Publication
Publication ID: 16978046
Legewie S, Blüthgen N, Herzel H.
Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability.
PLoS Comput. Biol. 2006 Sep; 2(9): e120
Institute for Theoretical Biology, Humboldt University, Berlin, Germany. s.legewie@biologie.hu-berlin.de  [more]
Model
Original Model: BIOMD0000000102.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL8567576821
Submission Date: 23 Mar 2007 10:57:49 UTC
Last Modification Date: 05 Mar 2014 16:59:25 UTC
Creation Date: 20 Apr 2006 10:59:50 UTC
Encoders:  Harish Dharuri
   Stefan Legewie
   Nils Bluethgen
   Hanspeter Herzel
set #1
bqbiol:isVersionOf Gene Ontology apoptotic process
set #2
bqbiol:isPartOf KEGG Pathway hsa04210
set #3
bqbiol:hasTaxon Taxonomy cellular organisms
Notes

The model reproduces active Caspase-3 time profile corresponding to the total Apaf-1 value of 20 nM as depicted in Fig 2-A . The model was successfully tested on MathSBML.

Model
Publication ID: 16978046 Submission Date: 23 Mar 2007 10:57:49 UTC Last Modification Date: 05 Mar 2014 16:59:25 UTC Creation Date: 20 Apr 2006 10:59:50 UTC
Mathematical expressions
Reactions
Caspase 9 / Apaf-1 binding Caspase 3 cleavage by Caspase 9 Caspase 3 cleavage by Caspase 9-Apaf-1 Caspase 9 Xiap binding
Caspase 9-Apaf-1 Xiap binding Caspase 9-Xiap Apaf-1 binding cleaved Caspase 3-Xiap binding Caspase 9 cleavage by cleaved caspase 3
Caspase 9 cleavage by cleaved caspase 3 when Apaf-1 is bound cleaved Caspase 9 Apaf-1 binding cleaved Caspase 9 XIAP binding cleaved Caspase 9-Apaf-1 XIAP binding
cleaved Caspase 9-Xiap Apaf-1 binding Caspase 3 cleavage by cleaved Caspase 9 Caspase 3 cleavage by cleaved Caspase 9 - Apaf-1 Apaf-1 turnover
Caspase 9 turnover Xiap turnover Caspase 9-Xiap degradation Apaf-1-Caspase 9-Xiap degradation
Apaf-1-Caspase 9 degradation Caspase 3 turnover Caspase 3 cleaved degradation Caspase 3 cleaved-Xiap degradation
Caspase 9 cleaved-Xiap degradation Caspase 9 cleaved degradation Apaf-1 Caspase 9 cleaved degradation Apaf-1 Caspase 9 cleaved-Xiap degradation
Physical entities
Compartments Species
Cytosol APAF-1 Caspase 9 Caspase 9-XIAP complex
XIAP APAF-1-Caspase 9-XIAP complex APAF-1-Caspase 9 complex
Caspase 3 Caspase 3 cleaved Caspase 3 cleaved - XIAP complex
Caspase 9 cleaved-XIAP complex Caspase 9 cleaved APAF-1-Caspase 9 cleaved complex
Apaf-1-Caspase 9 cleaved -XIAP complex    
Global parameters
k1 kb1 k2 k3
k4 k5 k6 k7
k8 k8b k9 k9b
k10 k10b k11 k11b
k12 k12b k13 k13b
k14 k14b k15 k15b
k16 k16prod k17 k17prod
k18 k18prod k19 k20
k21 k22 k22prod k23
k24 k25 k26 k27
k28      
Reactions (28)
 
 Caspase 9 / Apaf-1 binding [APAF-1] + [Caspase 9] ↔ [APAF-1-Caspase 9 complex];  
 
 Caspase 3 cleavage by Caspase 9 [Caspase 3] + [Caspase 9] → [Caspase 3 cleaved] + [Caspase 9];  
 
 Caspase 3 cleavage by Caspase 9-Apaf-1 [Caspase 3] + [APAF-1-Caspase 9 complex] → [Caspase 3 cleaved] + [APAF-1-Caspase 9 complex];  
 
 Caspase 9 Xiap binding [Caspase 9] + [XIAP] ↔ [Caspase 9-XIAP complex];  
 
 Caspase 9-Apaf-1 Xiap binding [APAF-1-Caspase 9 complex] + [XIAP] ↔ [APAF-1-Caspase 9-XIAP complex];  
 
 Caspase 9-Xiap Apaf-1 binding [Caspase 9-XIAP complex] + [APAF-1] ↔ [APAF-1-Caspase 9-XIAP complex];  
 
 cleaved Caspase 3-Xiap binding [Caspase 3 cleaved] + [XIAP] ↔ [Caspase 3 cleaved - XIAP complex];  
 
 Caspase 9 cleavage by cleaved caspase 3 [Caspase 9] + [Caspase 3 cleaved] → [Caspase 9 cleaved] + [Caspase 3 cleaved];  
 
 Caspase 9 cleavage by cleaved caspase 3 when Apaf-1 is bound [APAF-1-Caspase 9 complex] + [Caspase 3 cleaved] → [APAF-1-Caspase 9 cleaved complex] + [Caspase 3 cleaved];  
 
 cleaved Caspase 9 Apaf-1 binding [Caspase 9 cleaved] + [APAF-1] ↔ [APAF-1-Caspase 9 cleaved complex];  
 
 cleaved Caspase 9 XIAP binding [Caspase 9 cleaved] + [XIAP] ↔ [Caspase 9 cleaved-XIAP complex];  
 
 cleaved Caspase 9-Apaf-1 XIAP binding [APAF-1-Caspase 9 cleaved complex] + [XIAP] ↔ [Apaf-1-Caspase 9 cleaved -XIAP complex];  
 
 cleaved Caspase 9-Xiap Apaf-1 binding [Caspase 9 cleaved-XIAP complex] + [APAF-1] ↔ [Apaf-1-Caspase 9 cleaved -XIAP complex];  
 
 Caspase 3 cleavage by cleaved Caspase 9 [Caspase 3] + [Caspase 9 cleaved] → [Caspase 3 cleaved] + [Caspase 9 cleaved];  
 
 Caspase 3 cleavage by cleaved Caspase 9 - Apaf-1 [Caspase 3] + [APAF-1-Caspase 9 cleaved complex] → [Caspase 3 cleaved] + [APAF-1-Caspase 9 cleaved complex];  
 
 Apaf-1 turnover  → [APAF-1];  
 
 Caspase 9 turnover  → [Caspase 9];  
 
 Xiap turnover  → [XIAP];  
 
 Caspase 9-Xiap degradation [Caspase 9-XIAP complex] → ;  
 
 Apaf-1-Caspase 9-Xiap degradation [APAF-1-Caspase 9-XIAP complex] → ;  
 
 Apaf-1-Caspase 9 degradation [APAF-1-Caspase 9 complex] → ;  
 
 Caspase 3 turnover  → [Caspase 3];  
 
 Caspase 3 cleaved degradation [Caspase 3 cleaved] → ;  
 
 Caspase 3 cleaved-Xiap degradation [Caspase 3 cleaved - XIAP complex] → ;  
 
 Caspase 9 cleaved-Xiap degradation [Caspase 9 cleaved-XIAP complex] → ;  
 
 Caspase 9 cleaved degradation [Caspase 9 cleaved] → ;  
 
 Apaf-1 Caspase 9 cleaved degradation [APAF-1-Caspase 9 cleaved complex] → ;  
 
 Apaf-1 Caspase 9 cleaved-Xiap degradation [Apaf-1-Caspase 9 cleaved -XIAP complex] → ;  
 
 Cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 APAF-1
Compartment: Cytosol
Initial concentration: 20.0
 
 Caspase 9
Compartment: Cytosol
Initial concentration: 20.0
 
 Caspase 9-XIAP complex
Compartment: Cytosol
Initial concentration: 0.0
 
 XIAP
Compartment: Cytosol
Initial concentration: 40.0
 
 APAF-1-Caspase 9-XIAP complex
Compartment: Cytosol
Initial concentration: 0.0
 
 APAF-1-Caspase 9 complex
Compartment: Cytosol
Initial concentration: 0.0
 
 Caspase 3
Compartment: Cytosol
Initial concentration: 200.0
 
 Caspase 3 cleaved
Compartment: Cytosol
Initial concentration: 0.0
 
 Caspase 3 cleaved - XIAP complex
Compartment: Cytosol
Initial concentration: 0.0
 
 Caspase 9 cleaved-XIAP complex
Compartment: Cytosol
Initial concentration: 0.0
 
 Caspase 9 cleaved
Compartment: Cytosol
Initial concentration: 0.0
 
 APAF-1-Caspase 9 cleaved complex
Compartment: Cytosol
Initial concentration: 0.0
 
 Apaf-1-Caspase 9 cleaved -XIAP complex
Compartment: Cytosol
Initial concentration: 0.0
 
Global Parameters (41)
 
   k1
Value: 0.0020   (Units: per_nM_per_sec)
Constant
 
   kb1
Value: 0.1   (Units: sec_inverse)
Constant
 
   k2
Value: 5.0E-6   (Units: per_nM_per_sec)
Constant
 
   k3
Value: 3.5E-4   (Units: per_nM_per_sec)
Constant
 
   k4
Value: 2.0E-4   (Units: per_nM_per_sec)
Constant
 
   k5
Value: 2.0E-4   (Units: per_nM_per_sec)
Constant
 
   k6
Value: 5.0E-5   (Units: per_nM_per_sec)
Constant
 
   k7
Value: 0.0035   (Units: per_nM_per_sec)
Constant
 
   k8
Value: 0.0020   (Units: per_nM_per_sec)
Constant
 
   k8b
Value: 0.1   (Units: sec_inverse)
Constant
 
   k9
Value: 0.0010   (Units: per_nM_per_sec)
Constant
 
   k9b
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k10
Value: 0.0010   (Units: per_nM_per_sec)
Constant
 
   k10b
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k11
Value: 0.0010   (Units: per_nM_per_sec)
Constant
 
   k11b
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k12
Value: 0.0010   (Units: per_nM_per_sec)
Constant
 
   k12b
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k13
Value: 0.0020   (Units: per_nM_per_sec)
Constant
 
   k13b
Value: 0.1   (Units: sec_inverse)
Constant
 
   k14
Value: 0.0020   (Units: per_nM_per_sec)
Constant
 
   k14b
Value: 0.1   (Units: sec_inverse)
Constant
 
   k15
Value: 0.0030   (Units: per_nM_per_sec)
Constant
 
   k15b
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k16
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k16prod
Value: 0.02   (Units: nM_per_sec)
Constant
 
   k17
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k17prod
Value: 0.02   (Units: nM_per_sec)
Constant
 
   k18
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k18prod
Value: 0.04   (Units: nM_per_sec)
Constant
 
   k19
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k20
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k21
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k22
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k22prod
Value: 0.2   (Units: nM_per_sec)
Constant
 
   k23
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k24
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k25
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k26
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k27
Value: 0.0010   (Units: sec_inverse)
Constant
 
   k28
Value: 0.0010   (Units: sec_inverse)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000102

Curator's comment: (updated: 22 Mar 2007 23:30:25 GMT)

The simulation image shown corresponds to active caspase-3 temporal evolution for Apaf-1 concentration of 20nM as depicted in Fig-2A of the paper. Result obtained from MathSBML.

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