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BIOMD0000000112 - Clarke2006_Smad_signalling

 

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Reference Publication
Publication ID: 17186703
Clarke DC, Betterton MD, Liu X.
Systems theory of Smad signalling.
Syst Biol (Stevenage) 2006 Nov; 153(6): 412-424
Department of Chemistry and Biochemistry , University of Colorado-Boulder, Boulder, CO 80309, USA.  [more]
Model
Original Model: BIOMD0000000112.xml.origin
Submitter: Katja Wegner
Submission ID: MODEL4024559990
Submission Date: 23 Apr 2007 23:24:16 UTC
Last Modification Date: 29 Oct 2010 21:55:44 UTC
Creation Date: 29 Nov 2006 19:35:49 UTC
Encoders:  Harish Dharuri
   Katja Wegner
set #1
bqbiol:is Gene Ontology transforming growth factor beta receptor signaling pathway
bqbiol:isPartOf KEGG Pathway hsa04350
bqbiol:occursIn Taxonomy Neovison vison
Notes

The model reproduces the temporal evolution of four variables depicted in Fig 2a. The solution is generated for median parameter values as given in Table 3. Result shown was generated by MathSBML.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels.net Team.
For more information see the terms of use .
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.

Model
Publication ID: 17186703 Submission Date: 23 Apr 2007 23:24:16 UTC Last Modification Date: 29 Oct 2010 21:55:44 UTC Creation Date: 29 Nov 2006 19:35:49 UTC
Mathematical expressions
Reactions
Phosphorylation R-Smad translocation Smad4 translocation Complex formation
Complex translocation Complex in nucleus Dephosphorylation Receptor degradation
Rules
Assignment Rule (variable: sum_R_smad_nuc) Assignment Rule (variable: sum_Smad4_nuc) Assignment Rule (variable: sum_R_smad_cyt) Assignment Rule (variable: sum_Smad4_cyt)
Physical entities
Compartments Species
cytoplasm receptors R-Smad_cyt R-Smad-P_cyt
Smad4_cyt R-Smad-P-Smad4_cyt  
nucleus R-Smad-P-Smad4_nuc R-Smad_nuc R-Smad-P_nuc
Smad4_nuc Pi  
Global parameters
sum_R_smad_cyt sum_R_smad_nuc sum_Smad4_cyt sum_Smad4_nuc
Reactions (8)
 
 Phosphorylation [R-Smad_cyt] → [R-Smad-P_cyt];   {receptors}
 
 R-Smad translocation [R-Smad_nuc] ↔ [R-Smad_cyt];  
 
 Smad4 translocation [Smad4_nuc] ↔ [Smad4_cyt];  
 
 Complex formation [R-Smad-P_cyt] + [Smad4_cyt] ↔ [R-Smad-P-Smad4_cyt];  
 
 Complex translocation [R-Smad-P-Smad4_cyt] → [R-Smad-P-Smad4_nuc];  
 
 Complex in nucleus [R-Smad-P-Smad4_nuc] ↔ [Smad4_nuc] + [R-Smad-P_nuc];  
 
 Dephosphorylation [R-Smad-P_nuc] → [R-Smad_nuc] + [Pi];  
 
 Receptor degradation [receptors] → ;  
 
Rules (4)
 
 Assignment Rule (name: sum_R_smad_nuc) sum_R_smad_nuc = R_smad_nuc+R_smad_P_nuc+R_smad_P_smad4_nuc
 
 Assignment Rule (name: sum_smad4_nuc) sum_Smad4_nuc = smad4_nuc+R_smad_P_smad4_nuc
 
 Assignment Rule (name: sum_R_smad_cyt) sum_R_smad_cyt = R_smad_cyt+R_smad_P_cyt+R_smad_P_smad4_cyt
 
 Assignment Rule (name: sum_smad4_cyt) sum_Smad4_cyt = smad4_cyt+R_smad_P_smad4_cyt
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 receptors
Compartment: cytoplasm
Initial amount: 10000.0
 
 R-Smad_cyt
Compartment: cytoplasm
Initial amount: 162000.0
 
 R-Smad-P_cyt
Compartment: cytoplasm
Initial amount: 0.0
 
 Smad4_cyt
Compartment: cytoplasm
Initial amount: 120000.0
 
 R-Smad-P-Smad4_cyt
Compartment: cytoplasm
Initial amount: 0.0
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 R-Smad-P-Smad4_nuc
Compartment: nucleus
Initial amount: 0.0
 
 R-Smad_nuc
Compartment: nucleus
Initial amount: 18000.0
 
 R-Smad-P_nuc
Compartment: nucleus
Initial amount: 0.0
 
 Smad4_nuc
Compartment: nucleus
Initial amount: 30000.0
 
 Pi
Compartment: nucleus
Initial amount: 0.0
 
Global Parameters (4)
 
   sum_R_smad_cyt  
 
   sum_R_smad_nuc  
 
   sum_Smad4_cyt  
 
   sum_Smad4_nuc  
 
Phosphorylation (2)
 
   KCAT
Value: 3.51   (Units: min_inv)
Constant
 
   K1
Value: 289000.0   (Units: substance)
Constant
 
R-Smad translocation (2)
 
   k5nc
Value: 5.63   (Units: min_inv)
Constant
 
   k5cn
Value: 0.563   (Units: min_inv)
Constant
 
Smad4 translocation (2)
 
   k4nc
Value: 0.783   (Units: min_inv)
Constant
 
   k4cn
Value: 0.00497   (Units: min_inv)
Constant
 
Complex formation (2)
 
   k2a
Value: 6.5E-5   (Units: per item per min)
Constant
 
   k2d
Value: 0.0399   (Units: min_inv)
Constant
 
Complex translocation (1)
 
   k3
Value: 16.6   (Units: min_inv)
Constant
 
Complex in nucleus (2)
 
   k6d
Value: 0.0492   (Units: min_inv)
Constant
 
   k6a
Value: 1.44E-4   (Units: per item per min)
Constant
 
Dephosphorylation (2)
 
   Vmax7
Value: 17100.0   (Units: items per min)
Constant
 
   K7
Value: 8950.0   (Units: substance)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000112

Curator's comment: (updated: 23 Apr 2007 15:17:17 PDT)

Model solution shown above was generated by MathSBML and corresponds to Fig 2a of the paper.

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