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BIOMD0000000113 - Dupont1992_Ca_dpt_protein_phospho

 

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Reference Publication
Publication ID: 1316185
Dupont G, Goldbeter A.
Protein phosphorylation driven by intracellular calcium oscillations: a kinetic analysis.
Biophys. Chem. 1992 Apr; 42(3): 257-270
Faculté des Sciences, Université Libre de Bruxelles, Belgium.  [more]
Model
Original Model: BIOMD0000000113.origin
Submitter: Harish Dharuri
Submission ID: MODEL7007141507
Submission Date: 23 Apr 2007 15:26:51 UTC
Last Modification Date: 06 Apr 2014 22:00:52 UTC
Creation Date: 19 Apr 2007 10:14:36 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:is Gene Ontology inositol phosphate-mediated signaling
Gene Ontology calcium-mediated signaling
bqbiol:hasTaxon Taxonomy cellular organisms
Notes

Model reproduces Fig 4 of the paper. For fraction of phosphorylated protein, W_star, the model reproduces panel b in the same figure. Model successfully tested on MathSBML and Jarnac.


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: 1316185 Submission Date: 23 Apr 2007 15:26:51 UTC Last Modification Date: 06 Apr 2014 22:00:52 UTC Creation Date: 19 Apr 2007 10:14:36 UTC
Mathematical expressions
Reactions
Calcium influx InsP3 dependent Ca influx ATP driven pumping of Ca into store ATP driven pumping into cytosol
Calcium leak Ca efflux Protein Phosphorylation  
Rules
Assignment Rule (variable: vk)      
Physical entities
Compartments Species
cytosol Z Total Protein Phosphorylated protein
store Y    
Global parameters
v0 Vm2 n Kp
Vm3 m Kr K_A
kf k p vk
vMK vp Ka q
K1 K2 v1_beta  
Reactions (7)
 
 Calcium influx  → [Z];  
 
 InsP3 dependent Ca influx  → [Z];  
 
 ATP driven pumping of Ca into store [Z] → [Y];  
 
 ATP driven pumping into cytosol [Y] → [Z];  
 
 Calcium leak [Y] → [Z];  
 
 Ca efflux [Z] → ;  
 
 Protein Phosphorylation  ↔ [Phosphorylated protein];   {Total Protein}
 
Rules (1)
 
 Assignment Rule (name: vk) vk = vMK*Z^q/(Ka^q+Z^q)
 
 cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 Z
Compartment: cytosol
Initial concentration: 0.15
 
   Total Protein
Compartment: cytosol
Initial concentration: 1.0
 
   Phosphorylated protein
Compartment: cytosol
 
 store Spatial dimensions: 3.0  Compartment size: 1.0
 
 Y
Compartment: store
Initial concentration: 1.6
 
Global Parameters (19)
 
   v0
Value: 1.0
Constant
 
   Vm2
Value: 65.0
Constant
 
   n
Value: 2.0
Constant
 
   Kp
Value: 1.0
Constant
 
   Vm3
Value: 500.0
Constant
 
   m
Value: 2.0
Constant
 
   Kr
Value: 2.0
Constant
 
   K_A
Value: 0.9
Constant
 
   kf
Value: 1.0
Constant
 
   k
Value: 10.0
Constant
 
   p
Value: 4.0
Constant
 
   vk
Value: NaN
 
   vMK
Value: 20.0
 
   vp
Value: 2.5
Constant
 
   Ka
Value: 2.5
Constant
 
   q
Value: 1.0
Constant
 
   K1
Value: 0.01
Constant
 
   K2
Value: 0.01
Constant
 
   v1_beta
Value: 2.7
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000113

Curator's comment: (updated: 19 Apr 2007 19:27:29 BST)

Shown above are plots that reproduce Fig 4 of the paper. Result shown was generated by MathSBML.

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