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BIOMD0000000120 - Chan2004_TCell_receptor_activation

 

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Reference Publication
Publication ID: 15255048
Chan C, Stark J, George AJ.
Feedback control of T-cell receptor activation.
Proc. Biol. Sci. 2004 May; 271(1542): 931-939
Department of Immunology, Division of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK.  [more]
Model
Original Model: BIOMD0000000120.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL2514697386
Submission Date: 22 Jun 2007 13:02:10 UTC
Last Modification Date: 05 Jul 2012 14:45:43 UTC
Creation Date: 22 Jun 2007 01:48:34 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf KEGG Pathway hsa04660
Gene Ontology regulation of T cell receptor signaling pathway
bqbiol:occursIn Taxonomy cellular organisms
Notes

The model reproduces Fig 3a of the paper. Please note that the authors mention that they used a value of 2 for n, n being the power in the positive feedback function for kinase autocatalysis, however the model here has n=1.95 because this results in a simulation that is identical to Fig 3a. The model was successfully tested on MathSBML.


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: 15255048 Submission Date: 22 Jun 2007 13:02:10 UTC Last Modification Date: 05 Jul 2012 14:45:43 UTC Creation Date: 22 Jun 2007 01:48:34 UTC
Mathematical expressions
Reactions
Kinase recruitment to T-cell receptor Kinase inactivation Basal kinase activation Catalytic kinase activation
Inactive kinase diffusion Active kinase diffusion Basal phosphatase activation Catalyzed phosphatase activation
Phosphatase inactivation Active phosphatase diffusion    
Rules
Assignment Rule (variable: Total kinase)      
Events
Setting r(l) to 1 Resetting r(l) to 0    
Physical entities
Compartments Species
cell Inactive lck Active lck Inactive phosphatase
Active phosphatase Total kinase  
Global parameters
n1 k1 m1 d0
d1 k2 m2 n2
d2 n r_l  
Reactions (10)
 
 Kinase recruitment to T-cell receptor  → [Inactive lck];  
 
 Kinase inactivation [Active lck] → [Inactive lck];   {Active phosphatase}
 
 Basal kinase activation [Inactive lck] → [Active lck];  
 
 Catalytic kinase activation [Inactive lck] → [Active lck];  
 
 Inactive kinase diffusion [Inactive lck] → ;  
 
 Active kinase diffusion [Active lck] → ;  
 
 Basal phosphatase activation [Inactive phosphatase] → [Active phosphatase];  
 
 Catalyzed phosphatase activation [Inactive phosphatase] → [Active phosphatase];   {Active lck}
 
 Phosphatase inactivation [Active phosphatase] → [Inactive phosphatase];  
 
 Active phosphatase diffusion [Active phosphatase] → ;  
 
Rules (1)
 
 Assignment Rule (name: lck_total) Total kinase = lck_inactive+lck_active
 
Events (2)
 
 Setting r(l) to 1
r_l = 1
 
 Resetting r(l) to 0
r_l = 0
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Inactive lck
Compartment: cell
Initial amount: 0.0
 
 Active lck
Compartment: cell
Initial amount: 0.0
 
 Inactive phosphatase
Compartment: cell
Initial amount: 0.6
 
 Active phosphatase
Compartment: cell
Initial amount: 0.6
 
  Total kinase
Compartment: cell
Initial amount: 0.0
 
Global Parameters (11)
 
   n1
Value: 1.0   (Units: per_sec_per_item)
Constant
 
   k1
Value: 0.01   (Units: sec_inv)
Constant
 
   m1
Value: 1.0
Constant
 
   d0
Value: 0.15   (Units: sec_inv)
Constant
 
   d1
Value: 0.15   (Units: sec_inv)
Constant
 
   k2
Value: 0.01   (Units: sec_inv)
Constant
 
   m2
Value: 1.0   (Units: per_sec_per_item)
Constant
 
   n2
Value: 0.02   (Units: sec_inv)
Constant
 
   d2
Constant
 
   n
Value: 1.95   (Units: dimensionless)
Constant
 
   r_l  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000120

Curator's comment: (updated: 22 Jun 2007 13:20:12 BST)

The plot corresponds to Fig 3a of the paper. Simulation results obtained from MathSBML.

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