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BIOMD0000000329 - Kummer2000 - Oscillations in Calcium Signalling

 

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Reference Publication
Publication ID: 10968983
Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G.
Switching from simple to complex oscillations in calcium signaling.
Biophys. J. 2000 Sep; 79(3): 1188-1195
European Media Laboratory, 69118 Heidelberg, Germany. ursula.kummer@eml.villa-bosch.de  [more]
Model
Original Model: BIOMD0000000329.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1105060000
Submission Date: 06 May 2011 14:43:12 UTC
Last Modification Date: 11 Dec 2014 16:20:22 UTC
Creation Date: 11 Dec 2014 15:35:19 UTC
Encoders:  Vijayalakshmi Chelliah
   Pedro Mendes
   Ursula Kummer
set #1
bqbiol:hasTaxon Taxonomy Rattus norvegicus
set #2
bqbiol:isVersionOf Gene Ontology calcium-mediated signaling
set #3
bqbiol:occursIn Brenda Tissue Ontology hepatocyte
Notes
Kummer2000 - Oscillations in Calcium Signalling

Simplified (3-variable) calcium oscillation model Kummer et al. (2000) Biophys. J. 79, 1188-1195 This model is defined in a small compartment with low concentrations. You can run it first with the LSODA ODE solver and then with the Gillespie Monte Carlo method (in Time Course widget). This illustrates that at low particle numbers, as here, the stochastic simulation and the ODE approach produce different results (the stochastic approach is more correct in these circumstances). This file also demonstrates the use of several different plots to visualize results, including a histogram.

This model is described in the article:

Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G.
Biophys. J. 2000 Sep; 79(3): 1188-1195

Abstract:

We present a new model for calcium oscillations based on experiments in hepatocytes. The model considers feedback inhibition on the initial agonist receptor complex by calcium and activated phospholipase C, as well as receptor type-dependent self-enhanced behavior of the activated G(alpha) subunit. It is able to show simple periodic oscillations and periodic bursting, and it is the first model to display chaotic bursting in response to agonist stimulations. Moreover, our model offers a possible explanation for the differences in dynamic behavior observed in response to different agonists in hepatocytes.

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.

Model
Publication ID: 10968983 Submission Date: 06 May 2011 14:43:12 UTC Last Modification Date: 11 Dec 2014 16:20:22 UTC Creation Date: 11 Dec 2014 15:35:19 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
Physical entities
Compartments Species
compartment G-alpha activePLC Calcium
Reactions (8)
 
 R1  → [G-alpha];  
 
 R2  → [G-alpha];   {G-alpha}
 
 R3 [G-alpha] → ;   {activePLC}
 
 R4 [G-alpha] → ;   {Calcium}
 
 R5  → [activePLC];   {G-alpha}
 
 R6 [activePLC] → ;  
 
 R7  → [Calcium];   {G-alpha}
 
 R8 [Calcium] → ;  
 
Functions (4)
 
 Constant flux (irreversible) lambda(v, v)
 
 Henri-Michaelis-Menten (irreversible) lambda(substrate, Km, V, V*substrate/(Km+substrate))
 
 Irr Michaelis-Menten (enzyme)[userdefined] lambda(V, E, S, Km, V*E*S/(Km+S))
 
 linear activation lambda(constant, Activator, constant*Activator)
 
 compartment Spatial dimensions: 3.0  Compartment size: 1.0E-13
 
 G-alpha
Compartment: compartment
Initial concentration: 0.01
 
 activePLC
Compartment: compartment
Initial concentration: 0.01
 
 Calcium
Compartment: compartment
Initial concentration: 0.01
 
R1 (1)
 
   v
Value: 0.212
Constant
 
R2 (1)
 
   constant
Value: 2.9
Constant
 
R3 (2)
 
   V
Value: 1.52
Constant
 
   Km
Value: 0.19
Constant
 
R4 (2)
 
   V
Value: 4.88
Constant
 
   Km
Value: 1.18
Constant
 
R5 (1)
 
   constant
Value: 1.24
Constant
 
R6 (2)
 
   Km
Value: 29.09
Constant
 
   V
Value: 32.24
Constant
 
R7 (1)
 
   constant
Value: 13.58
Constant
 
R8 (2)
 
   Km
Value: 0.16
Constant
 
   V
Value: 153.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000329

Curator's comment: (updated: 11 Dec 2014 16:14:18 GMT)

This model correspond to the core model (3 variable model defined by equations 6 to 8) of the reference publication. Figure 7 of the paper has been reproduced here. The simulation was done using Copasi v4.14 (Build 89) and the plot was generated using Gnuplot.

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