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BIOMD0000000122 - Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics

 

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Reference Publication
Publication ID: 17031595
Fisher WG, Yang PC, Medikonduri RK, Jafri MS.
NFAT and NFkappaB activation in T lymphocytes: a model of differential activation of gene expression.
Ann Biomed Eng 2006 Nov; 34(11): 1712-1728
Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.  [more]
Model
Original Model: BIOMD0000000122.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL2977476330
Submission Date: 05 Jul 2007 08:15:15 UTC
Last Modification Date: 14 Feb 2014 16:52:55 UTC
Creation Date: 26 Jun 2007 15:45:06 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf Gene Ontology regulation of T cell mediated immunity
bqbiol:isPartOf KEGG Pathway hsa04660
bqbiol:is Gene Ontology calcineurin-NFAT signaling cascade
bqbiol:hasTaxon Taxonomy Mammalia
set #2
bqbiol:occursIn Brenda Tissue Ontology BTO:0000782
Notes

The model reproduces the calcium oscillation dependent activation-deactivation kinetics of nuclear factor of activated T cells (NFAT) as depicted in Fig 4a of the paper. A simple algorithm in the events section takes care of the calcium oscillation. 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: 17031595 Submission Date: 05 Jul 2007 08:15:15 UTC Last Modification Date: 14 Feb 2014 16:52:55 UTC Creation Date: 26 Jun 2007 15:45:06 UTC
Mathematical expressions
Reactions
Calcineurin dpdnt NFAT dephosphorylation NFAT Calcineurin complex formation NFAT transport Active Calcineurin transport
NFAT Calcineurin complex phosphorylation Phosphorylated NFAT Calcineurin complex disassembly NFAT Calcineurin complex transport NFAT Calcineurin complex phosphorylation
Phosphorylated NFAT Calcineurin complex disassembly Phosphorylated NFAT transport NFAT Calcineurin complex disassembly Phosphorylated NFAT Calcineurin complex transport
Calcineurin dpdnt NFAT dephosphorylation Calcineurin activation Calcineurin activation Inactive Calcineurin transport
Calcium transport      
Events
event_0000001 event_0000002 event_0000003  
Physical entities
Compartments Species
cytosol Calcium in Cytosol NFAT_Cyt Active Calcineurin in cytosol
Phosphorylated NFAT in cytosol NFAT Calcineurin complex in cytosol Phosphorylated NFAT Calcineurin complex in cytosol
Inactive Calcineurin in cytosol    
nucleus Calcium in Nucleus NFAT_nuc Active Calcineurin in Nucleus
Phosphorylated NFAT in nucleus NFAT Calcineurin complex in nucleus Phosphorylated NFAT Calcineurin complex in nucleus
Inactive Calcineurin in nucleus    
Global parameters
k1 k2 k16 k15
k18 k17 k6 k5
k14 k13 k12 k11
k10 k9 k3 k4
k7 k8 k19 k20
k21 k22 Time_in_Seconds  
Reactions (17)
 
 Calcineurin dpdnt NFAT dephosphorylation [Phosphorylated NFAT in nucleus] + [Active Calcineurin in Nucleus] ↔ [Active Calcineurin in Nucleus] + [NFAT_nuc];  
 
 NFAT Calcineurin complex formation [Active Calcineurin in Nucleus] + [NFAT_nuc] ↔ [NFAT Calcineurin complex in nucleus];  
 
 NFAT transport [NFAT_nuc] ↔ [NFAT_Cyt];  
 
 Active Calcineurin transport [Active Calcineurin in Nucleus] ↔ [Active Calcineurin in cytosol];  
 
 NFAT Calcineurin complex phosphorylation [NFAT Calcineurin complex in nucleus] ↔ [Phosphorylated NFAT Calcineurin complex in nucleus];  
 
 Phosphorylated NFAT Calcineurin complex disassembly [Phosphorylated NFAT Calcineurin complex in nucleus] ↔ [Active Calcineurin in Nucleus] + [Phosphorylated NFAT in nucleus];  
 
 NFAT Calcineurin complex transport [NFAT Calcineurin complex in nucleus] ↔ [NFAT Calcineurin complex in cytosol];  
 
 NFAT Calcineurin complex phosphorylation [NFAT Calcineurin complex in cytosol] ↔ [Phosphorylated NFAT Calcineurin complex in cytosol];  
 
 Phosphorylated NFAT Calcineurin complex disassembly [Phosphorylated NFAT Calcineurin complex in cytosol] ↔ [Active Calcineurin in cytosol] + [Phosphorylated NFAT in cytosol];  
 
 Phosphorylated NFAT transport [Phosphorylated NFAT in cytosol] ↔ [Phosphorylated NFAT in nucleus];  
 
 NFAT Calcineurin complex disassembly [NFAT Calcineurin complex in cytosol] ↔ [Active Calcineurin in cytosol] + [NFAT_Cyt];  
 
 Phosphorylated NFAT Calcineurin complex transport [Phosphorylated NFAT Calcineurin complex in cytosol] ↔ [Phosphorylated NFAT Calcineurin complex in nucleus];  
 
 Calcineurin dpdnt NFAT dephosphorylation [Phosphorylated NFAT in cytosol] + [Active Calcineurin in cytosol] ↔ [Active Calcineurin in cytosol] + [NFAT_Cyt];  
 
 Calcineurin activation 3.0 × [Calcium in Cytosol] + [Inactive Calcineurin in cytosol] ↔ [Active Calcineurin in cytosol];  
 
 Calcineurin activation 3.0 × [Calcium in Nucleus] + [Inactive Calcineurin in nucleus] ↔ [Active Calcineurin in Nucleus];  
 
 Inactive Calcineurin transport [Inactive Calcineurin in cytosol] ↔ [Inactive Calcineurin in nucleus];  
 
 Calcium transport [Calcium in Cytosol] ↔ [Calcium in Nucleus];  
 
Events (3)
 
 event_0000001
Time_in_Seconds = Time_in_Seconds+100
Calcium in Cytosol = 1
Calcium in Nucleus = 1
 
 event_0000002
Calcium in Cytosol = 0.1
Calcium in Nucleus = 0.1
 
 event_0000003
Calcium in Cytosol = 0.1
Calcium in Nucleus = 0.1
 
 cytosol Spatial dimensions: 3.0  Compartment size: 2.69E-13
 
 Calcium in Cytosol
Compartment: cytosol
Initial concentration: 1.0
 
 NFAT_Cyt
Compartment: cytosol
Initial concentration: 1.101E-4
 
 Active Calcineurin in cytosol
Compartment: cytosol
Initial concentration: 9.1E-6
 
 Phosphorylated NFAT in cytosol
Compartment: cytosol
Initial concentration: 0.0094397
 
 NFAT Calcineurin complex in cytosol
Compartment: cytosol
Initial concentration: 6.1E-6
 
 Phosphorylated NFAT Calcineurin complex in cytosol
Compartment: cytosol
Initial concentration: 2.2E-6
 
 Inactive Calcineurin in cytosol
Compartment: cytosol
Initial concentration: 0.0097108
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.13E-13
 
 Calcium in Nucleus
Compartment: nucleus
Initial concentration: 1.0
 
 NFAT_nuc
Compartment: nucleus
Initial concentration: 5.219E-4
 
 Active Calcineurin in Nucleus
Compartment: nucleus
Initial concentration: 5.05E-5
 
 Phosphorylated NFAT in nucleus
Compartment: nucleus
Initial concentration: 2.272E-4
 
 NFAT Calcineurin complex in nucleus
Compartment: nucleus
Initial concentration: 9.477E-4
 
 Phosphorylated NFAT Calcineurin complex in nucleus
Compartment: nucleus
Initial concentration: 2.5E-6
 
 Inactive Calcineurin in nucleus
Compartment: nucleus
Initial concentration: 0.049198
 
Global Parameters (23)
 
   k1
Value: 2.56E-5
Constant
 
   k2
Value: 0.00256
Constant
 
   k16
Value: 6.63
Constant
 
   k15
Value: 0.00168
Constant
 
   k18
Value: 9.6E-4
Constant
 
   k17
Value: 0.0015
Constant
 
   k6
Value: 9.2E-4
Constant
 
   k5
Value: 0.0019
Constant
 
   k14
Value: 0.00256
Constant
 
   k13
Value: 0.5
Constant
 
   k12
Value: 0.00168
Constant
 
   k11
Value: 6.63
Constant
 
   k10
Value: 0.0050
Constant
 
   k9
Value: 0.5
Constant
 
   k3
Value: 0.0050
Constant
 
   k4
Value: 0.5
Constant
 
   k7
Value: 0.0050
Constant
 
   k8
Value: 0.5
Constant
 
   k19
Value: 1.0
Constant
 
   k20
Value: 1.0
Constant
 
   k21
Value: 0.21
Constant
 
   k22
Value: 0.5
Constant
 
   Time_in_Seconds
Value: 100.0
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000122

Curator's comment: (updated: 28 Jun 2007 16:38:38 BST)

The plot corresponds to Fig 4a of the paper. Simulation result obtained from MathSBML.

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