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BIOMD0000000101 - Vilar2006_TGFbeta

  
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Reference Publication
Publication ID: 16446785
Vilar JM, Jansen R, Sander C.
Signal processing in the TGF-beta superfamily ligand-receptor network.
PLoS Comput Biol 2006 Jan;2(1):e3.
Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America. vilar@cbio.mskcc.org  [more]
Model
Original Model: BIOMD0000000101.xml.origin
Submitter: Katja Wegner
Submission ID: MODEL4023382414
Submission Date: 22 Mar 2007 22:55:11 UTC
Last Modification Date: 21 Aug 2008 12:15:44 UTC
Creation Date: 28 Nov 2006 18:39:38 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasPart KEGG Pathway hsa04350
set #2
bqbiol:hasPart Reactome REACT_6844.3
set #3
bqbiol:isVersionOf Gene Ontology transforming growth factor beta receptor signaling pathway
Notes

The model reproduces Fig 5A of the paper. The ligand concentration is increased from 3E-5 to 0.01 at time t=2500 to ensure that the system reaches steady state. Hence, the time t=0 of the paper corresponds to t=2500 in the model. The peak value of the active ligand receptor complex is off by a value of 1.25, the authors have stated that this discrepancy is due to the fact that the figure in the paper corresponds to a slightly different parameter set. The model was successfully tested on MathSBML.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 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: 16446785 Submission Date: 22 Mar 2007 22:55:11 UTC Last Modification Date: 21 Aug 2008 12:15:44 UTC Creation Date: 28 Nov 2006 18:39:38 UTC
Mathematical expressions
Reactions
Ligand receptor complex formation Ligand receptor complex constitutive degradation Ligand independent complex degradation Ligand receptor complex internalization
RI synthesis RI constitutive degradation RI internalization RI recycling
Ligand Receptor complex recycling RII synthesis RII constitutive degradation RII internalization
RII recycling      
Events
event_0000001      
Physical entities
Compartments Species
Plasma membrane Receptor 1 Receptor 2 ligand receptor complex-plasma membrane
     
Endosome ligand receptor complex-endosome Receptor 1-endosome Receptor 2 endosome
Global parameters
ka ligand kcd klid
ki pRI kr alpha
pRII      
Reactions (13)
 
 Ligand receptor complex formation [Receptor 2] + [Receptor 1] → [ligand receptor complex-plasma membrane];  
 
 Ligand receptor complex constitutive degradation [ligand receptor complex-plasma membrane] → ;  
 
 Ligand independent complex degradation [ligand receptor complex-plasma membrane] → ;  
 
 Ligand receptor complex internalization [ligand receptor complex-plasma membrane] → [ligand receptor complex-endosome];  
 
 RI synthesis  → [Receptor 1];  
 
 RI constitutive degradation [Receptor 1] → ;  
 
 RI internalization [Receptor 1] → [Receptor 1-endosome];  
 
 RI recycling [Receptor 1-endosome] → [Receptor 1];  
 
 Ligand Receptor complex recycling [ligand receptor complex-endosome] → [Receptor 1] + [Receptor 2];  
 
 RII synthesis  → [Receptor 2];  
 
 RII constitutive degradation [Receptor 2] → ;  
 
 RII internalization [Receptor 2] → [Receptor 2 endosome];  
 
 RII recycling [Receptor 2 endosome] → [Receptor 2];  
 
Events (1)
 
 event_0000001
ligand = 0.01
 
 Plasma membrane Spatial dimensions: 3  Compartment size: 1.0
 
 Receptor 1
Compartment: Plasma membrane
Initial amount: 20.0
 
 Receptor 2
Compartment: Plasma membrane
Initial amount: 20.0
 
 ligand receptor complex-plasma membrane
Compartment: Plasma membrane
Initial amount: 0.0
 
 Endosome Spatial dimensions: 3  Compartment size: 1.0
 
 ligand receptor complex-endosome
Compartment: Endosome
Initial amount: 40.0
 
 Receptor 1-endosome
Compartment: Endosome
Initial amount: 0.0
 
 Receptor 2 endosome
Compartment: Endosome
Initial amount: 0.0
 
Global Parameters (9)
 
   ka
Value: 1.0
Constant
 
   ligand
Value: 3.0E-5
 
   kcd
Value: 0.0277777778
Constant
 
   klid
Value: 0.25
Constant
 
   ki
Value: 0.3333333333333
Constant
 
   pRI
Value: 8.0
Constant
 
   kr
Value: 0.0333333333333333
Constant
 
   alpha
Value: 1.0
Constant
 
   pRII
Value: 4.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000101

Curator's comment: (updated: 01 May 2007 21:56:32 BST)

Simulation result corresponds to Fig 5A of the paper. Plot generated by MathSBML.
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