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BIOMD0000000329 - Kummer2000_CalciumSpiking

 

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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.xml.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1105060000
Submission Date: 06 May 2011 14:43:12 UTC
Last Modification Date: 11 Jul 2011 12:26:25 UTC
Creation Date: 05 May 2011 12:59:47 UTC
Encoders:  Vijayalakshmi Chelliah
set #1
bqbiol:occursIn Taxonomy Rattus norvegicus
Cell Type Ontology CL:0000182
set #2
bqbiol:isVersionOf Gene Ontology calcium-mediated signaling
Notes

This model is from the article:
Switching from simple to complex oscillations in calcium signaling.
Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G. Biophys J. 2000 Sep;79(3):1188-95. 10968983 ,
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.

Model
Publication ID: 10968983 Submission Date: 06 May 2011 14:43:12 UTC Last Modification Date: 11 Jul 2011 12:26:25 UTC Creation Date: 05 May 2011 12:59:47 UTC
Mathematical expressions
Rules
Rate Rule (variable: G-alpha) Rate Rule (variable: PLC) Rate Rule (variable: Calcium-Cyt) Rate Rule (variable: Calcium-ER)
Physical entities
Compartments Species
cytoplasm G-alpha PLC Calcium-Cyt
     
ER Calcium-ER    
Global parameters
k1 k2 k3 K4
k5 K6 k7 k8
K9 k10 K11 k12
k13 k14 K15 k16
K17      
Reactions (0)
Rules (4)
 
 Rate Rule (name: a) d [ G-alpha] / d t= k1+k2*a-k3*a*b/(a+K4)-k5*a*c/(a+K6)
 
 Rate Rule (name: b) d [ PLC] / d t= k7*a-k8*b/(b+K9)
 
 Rate Rule (name: c) d [ Calcium-Cyt] / d t= k10*c*b*d/(d+K11)+k12*b+k13*a-k14*c/(c+K15)-k16*c/(c+K17)
 
 Rate Rule (name: d) d [ Calcium-ER] / d t= (-k10)*c*b*d/(d+K11)+k16*c/(c+K17)
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 G-alpha
Compartment: cytoplasm
Initial concentration: 0.01
 
 PLC
Compartment: cytoplasm
Initial amount: 0.01
 
 Calcium-Cyt
Compartment: cytoplasm
Initial amount: 0.01
 
 ER Spatial dimensions: 3.0  Compartment size: 1.0
 
 Calcium-ER
Compartment: ER
Initial amount: 20.0
 
Global Parameters (17)
 
 k1
Value: 0.09
Constant
 
 k2
Value: 1.3
Constant
 
 k3
Value: 0.64
Constant
 
 K4
Value: 0.19
Constant
 
 k5
Value: 4.88
Constant
 
 K6
Value: 1.18
Constant
 
 k7
Value: 2.08
Constant
 
 k8
Value: 32.24
Constant
 
 K9
Value: 29.09
Constant
 
 k10
Value: 5.0
Constant
 
 K11
Value: 2.67
Constant
 
 k12
Value: 0.7
Constant
 
 k13
Value: 13.58
Constant
 
 k14
Value: 153.0
Constant
 
 K15
Value: 0.16
Constant
 
 k16
Value: 4.85
Constant
 
 K17
Value: 0.05
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000329

Curator's comment: (updated: 12 May 2011 12:08:55 BST)

Figure 3 of the reference publication has been reproduced here. Periodic and complex oscillations (bursting) of the free calcium (Cytoplasmic Calcium) in response to increasing degrees of agonist stimulation (k2). k2 varies from 1.3 to 2.7738, where for (a) k2 = 1.3, (b) k2 = 2.35, (c) k2 = 2.5, (d) k2 = 2.6 and (e) k2 = 2.7738.

The model was integrated and simulated using Copasi v4.6 (Build 32).

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