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BIOMD0000000163 - Zi2007_TGFbeta_signaling

 

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Reference Publication
Publication ID: 17895977
Zi Z, Klipp E.
Constraint-based modeling and kinetic analysis of the Smad dependent TGF-beta signaling pathway.
PLoS ONE 2007; 2(9): e936
Computational Systems Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.  [more]
Model
Original Model: Zi_PLoS ONE_TGF-beta
Submitter: Zhike Zi
Submission ID: MODEL3388742457
Submission Date: 25 Feb 2008 00:05:51 UTC
Last Modification Date: 05 Jul 2012 16:45:46 UTC
Creation Date: 14 Feb 2008 09:21:13 UTC
Encoders:  Harish Dharuri
   Edda Klipp
   Kun Yang
set #1
bqbiol:isPartOf KEGG Pathway hsa04350
bqbiol:isVersionOf Gene Ontology regulation of transforming growth factor beta receptor signaling pathway
bqbiol:occursIn Taxonomy cellular organisms
Notes

The model reproduces the time profiles of Total Smad2 in the nucleus as well as the cytoplasm as depicted in 2D and also the other time profiles as depicted in Fig 2. Two parameters that are not present in the paper are introduced here for illustration purposes and they are Total Smad2n and Total Smad2c. The term kr_EE*LRC_EE has not been included in the ODE's for T1R_surf, T2R_surf and TGFbeta in the paper but is included in this model. MathSBML was used to reproduce the simulation result.


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.

Model
Publication ID: 17895977 Submission Date: 25 Feb 2008 00:05:51 UTC Last Modification Date: 05 Jul 2012 16:45:46 UTC Creation Date: 14 Feb 2008 09:21:13 UTC
Mathematical expressions
Reactions
R1_Smad2_import R2_Smad2_export R3_Smad4_import R4_Smad4_export
R5_T1R_production R6_T1R_Cave_formation R7_T1R_Cave_recycling R8_T1R_EE_formation
R9_T1R_EE_recycling R10_T1R_EE_degradation R11_T2R_production R12_T2R_Cave_formation
R13_T2R_Cave_recycling R14_T2R_EE_formation R15_T2R_EE_recycling R16_T2R_EE_degradation
R17_LRC_formation R18_LRC_Cave_formation R19_LRC_Cave_recycling R20_LRC_EE_formation
R21_LRC_EE_recycling R22_LRC_EE_degradation R23_Smads_Complex_formation R24_Smads_Complex_import
R25_Smads_Complex_Dissociation R26_LRC_Cave_degradation    
Rules
Assignment Rule (variable: Total_Smad2n) Assignment Rule (variable: Total_Smad2c)    
Physical entities
Compartments Species
Medium TGF_beta    
Nucleus Smad2n Smad4n Smads_Complex_n
     
Cytoplasm Smad2c Smad4c T1R_Surf
T1R_Cave T1R_EE T2R_Surf
T2R_Cave T2R_EE LRC_Surf
LRC_Cave LRC_EE Smads_Complex_c
     
Global parameters
v_T1R v_T2R ki_EE kr_EE
ki_Cave kr_Cave Kcd k_LRC
Klid Kdeg_T1R_EE Kdeg_T2R_EE Kimp_Smad2c
Kexp_Smad2n Kimp_Smad4c Kexp_Smad4n k_Smads_Complex_c
Kimp_Smads_Complex_c Kdiss_Smads_Complex_n Total_Smad2n Total_Smad2c
Reactions (26)
 
 R1_Smad2_import [Smad2c] → [Smad2n];  
 
 R2_Smad2_export [Smad2n] → [Smad2c];  
 
 R3_Smad4_import [Smad4c] → [Smad4n];  
 
 R4_Smad4_export [Smad4n] → [Smad4c];  
 
 R5_T1R_production  → [T1R_Surf];  
 
 R6_T1R_Cave_formation [T1R_Surf] → [T1R_Cave];  
 
 R7_T1R_Cave_recycling [T1R_Cave] → [T1R_Surf];  
 
 R8_T1R_EE_formation [T1R_Surf] → [T1R_EE];  
 
 R9_T1R_EE_recycling [T1R_EE] → [T1R_Surf];  
 
 R10_T1R_EE_degradation [T1R_EE] → ;  
 
 R11_T2R_production  → [T2R_Surf];  
 
 R12_T2R_Cave_formation [T2R_Surf] → [T2R_Cave];  
 
 R13_T2R_Cave_recycling [T2R_Cave] → [T2R_Surf];  
 
 R14_T2R_EE_formation [T2R_Surf] → [T2R_EE];  
 
 R15_T2R_EE_recycling [T2R_EE] → [T2R_Surf] + [TGF_beta];  
 
 R16_T2R_EE_degradation [T2R_EE] → ;  
 
 R17_LRC_formation [TGF_beta] + [T2R_Surf] + [T1R_Surf] → [LRC_Surf];  
 
 R18_LRC_Cave_formation [LRC_Surf] → [LRC_Cave];  
 
 R19_LRC_Cave_recycling [LRC_Cave] → [T1R_Surf] + [TGF_beta] + [T2R_Surf];  
 
 R20_LRC_EE_formation [LRC_Surf] → [LRC_EE];  
 
 R21_LRC_EE_recycling [LRC_EE] → [T1R_Surf] + [T2R_Surf] + [TGF_beta];  
 
 R22_LRC_EE_degradation [LRC_EE] → ;  
 
 R23_Smads_Complex_formation [Smad2c] + [Smad4c] → [Smads_Complex_c];   {LRC_EE}
 
 R24_Smads_Complex_import [Smads_Complex_c] → [Smads_Complex_n];  
 
 R25_Smads_Complex_Dissociation [Smads_Complex_n] → [Smad4n] + [Smad2n];  
 
 R26_LRC_Cave_degradation [LRC_Cave] → ;   {Smads_Complex_n}
 
Rules (2)
 
 Assignment Rule (name: Total_Smad2n) Total_Smad2n = Smad2n+Smads_Complex_n
 
 Assignment Rule (name: Total_Smad2c) Total_Smad2c = Smad2c+Smads_Complex_c
 
 Medium Spatial dimensions: 3.0  Compartment size: 1.0
 
 TGF_beta
Compartment: Medium
Initial concentration: 0.08
 
 Nucleus Spatial dimensions: 3.0  Compartment size: 3.5E-4
 
 Smad2n
Compartment: Nucleus
Initial concentration: 236.45
 
 Smad4n
Compartment: Nucleus
Initial concentration: 551.72
 
 Smads_Complex_n
Compartment: Nucleus
Initial concentration: 0.0
 
 Cytoplasm Spatial dimensions: 3.0  Compartment size: 0.00105
 
 Smad2c
Compartment: Cytoplasm
Initial concentration: 492.61
 
 Smad4c
Compartment: Cytoplasm
Initial concentration: 1149.4
 
 T1R_Surf
Compartment: Cytoplasm
Initial concentration: 0.237
 
 T1R_Cave
Compartment: Cytoplasm
Initial concentration: 2.092
 
 T1R_EE
Compartment: Cytoplasm
Initial concentration: 2.06
 
 T2R_Surf
Compartment: Cytoplasm
Initial concentration: 0.202
 
 T2R_Cave
Compartment: Cytoplasm
Initial concentration: 1.778
 
 T2R_EE
Compartment: Cytoplasm
Initial concentration: 1.148
 
 LRC_Surf
Compartment: Cytoplasm
Initial concentration: 0.0
 
 LRC_Cave
Compartment: Cytoplasm
Initial concentration: 0.0
 
 LRC_EE
Compartment: Cytoplasm
Initial concentration: 0.0
 
 Smads_Complex_c
Compartment: Cytoplasm
Initial concentration: 0.0
 
Global Parameters (20)
 
   v_T1R
Value: 0.0103
Constant
 
   v_T2R
Value: 0.02869
Constant
 
   ki_EE
Value: 0.33
Constant
 
   kr_EE
Value: 0.033
Constant
 
   ki_Cave
Value: 0.33
Constant
 
   kr_Cave
Value: 0.03742
Constant
 
   Kcd
Value: 0.0050
Constant
 
   k_LRC
Value: 2197.0
 
   Klid
Value: 0.02609
Constant
 
   Kdeg_T1R_EE
Value: 0.0050
Constant
 
   Kdeg_T2R_EE
Value: 0.025
Constant
 
   Kimp_Smad2c
Value: 0.16
Constant
 
   Kexp_Smad2n
Value: 1.0
Constant
 
   Kimp_Smad4c
Value: 0.08
Constant
 
   Kexp_Smad4n
Value: 0.5
Constant
 
   k_Smads_Complex_c
Value: 6.85E-5
Constant
 
   Kimp_Smads_Complex_c
Value: 0.16
Constant
 
   Kdiss_Smads_Complex_n
Value: 0.1174
Constant
 
   Total_Smad2n  
 
   Total_Smad2c  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000163

Curator's comment: (updated: 20 Feb 2008 17:26:28 GMT)

The plot corresponds to Fig 2D of the paper. Result obtained from MathSBML.

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