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BIOMD0000000039 - Marhl2000_CaOscillations

 

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Reference Publication
Publication ID: 11004387
Marhl M, Haberichter T, Brumen M, Heinrich R.
Complex calcium oscillations and the role of mitochondria and cytosolic proteins.
BioSystems 2000 Jul; 57(2): 75-86
Department of Physics, Faculty of Education, University of Maribor, Koroska cesta 160, SI-2000, Maribor, Slovenia. marko.marhl@uni-mb.si  [more]
Model
Original Model: BIOMD0000000039.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL6621933497
Submission Date: 13 Sep 2005 14:32:40 UTC
Last Modification Date: 12 Feb 2014 14:17:17 UTC
Creation Date: 15 Jul 2005 09:10:44 UTC
Encoders:  Nicolas Le Novère
   Harish Dharuri
set #1
bqbiol:is KEGG Pathway hsa04020
Gene Ontology calcium-mediated signaling
Gene Ontology inositol phosphate-mediated signaling
bqbiol:occursIn Taxonomy Xenopus laevis
set #2
bqmodel:isDerivedFrom PubMed 17029696
PubMed 12362939
Notes

In order to reproduce the model, the volume of all compartment is set to 1, and the stoichiometry of CaER and CaM has been set to 0.25, corresponding to betaER/rhoER and betaM/rhoM described in the paper.


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: 11004387 Submission Date: 13 Sep 2005 14:32:40 UTC Last Modification Date: 12 Feb 2014 14:17:17 UTC Creation Date: 15 Jul 2005 09:10:44 UTC
Mathematical expressions
Reactions
Jch Jleak Jpump Jout
Jin dissociation of CaPr binding of Ca on Pr  
Physical entities
Compartments Species
Cytosol Ca_cyt CaPr Pr
Endoplasmic_Reticulum CaER    
Mitochondria CaM    
Reactions (7)
 
 Jch 0.25 × [CaER] → [Ca_cyt];   {Ca_cyt}
 
 Jleak 0.25 × [CaER] → [Ca_cyt];  
 
 Jpump [Ca_cyt] → 0.25 × [CaER];  
 
 Jout 0.25 × [CaM] → [Ca_cyt];   {Ca_cyt}
 
 Jin [Ca_cyt] → 0.25 × [CaM];   {Ca_cyt}
 
 dissociation of CaPr [CaPr] → [Pr] + [Ca_cyt];  
 
 binding of Ca on Pr [Pr] + [Ca_cyt] → [CaPr];  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_cyt
Compartment: Cytosol
Initial concentration: 0.35
 
 CaPr
Compartment: Cytosol
Initial concentration: 85.45
 
 Pr
Compartment: Cytosol
Initial concentration: 34.55
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 CaER
Compartment: Endoplasmic_Reticulum
Initial concentration: 0.76
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 CaM
Compartment: Mitochondria
Initial concentration: 0.29
 
Jch (2)
 
   Kch
Value: 4100.0
Constant
 
   K1
Value: 5.0
Constant
 
Jleak (1)
 
   Kleak
Value: 0.05
Constant
 
Jpump (1)
 
   Kpump
Value: 20.0
Constant
 
Jout (3)
 
   Kout
Value: 125.0
Constant
 
   K3
Value: 5.0
Constant
 
   Km
Value: 0.00625
Constant
 
Jin (2)
 
   Kin
Value: 300.0
Constant
 
   K2
Value: 0.8
Constant
 
dissociation of CaPr (1)
 
   Kminus
Value: 0.01
Constant
 
binding of Ca on Pr (1)
 
   Kplus
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000039

Curator's comment: (updated: 17 Dec 2006 11:12:29 GMT)

The figure reproduces Calcium bursting oscillations as depicted in Fig 2 of the paper. Simulation result obtained from Jarnac.

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