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BIOMD0000000330 - Larsen2004_CalciumSpiking

 

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Reference Publication
Publication ID: 14871603
Larsen AZ, Olsen LF, Kummer U.
On the encoding and decoding of calcium signals in hepatocytes.
Biophys. Chem. 2004 Jan; 107(1): 83-99
Celcom, Department of Biochemistry and Molecular Biology, Syddansk Universitet, Campusvej 55, Odense M DK-5230, Denmark. zahle@odense.kollegienet.dk  [more]
Model
Original Model: BIOMD0000000330.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1105060001
Submission Date: 06 May 2011 14:45:33 UTC
Last Modification Date: 28 May 2014 02:48:31 UTC
Creation Date: 05 May 2011 12:59:47 UTC
Encoders:  Vijayalakshmi Chelliah
set #1
bqmodel:isDerivedFrom BioModels Database Kummer2000_CalciumSpiking
set #2
bqbiol:occursIn Cell Type Ontology CL:0000182
set #3
bqbiol:isVersionOf Gene Ontology calcium-mediated signaling
set #4
bqbiol:hasTaxon Taxonomy Rattus norvegicus
Notes

This model is from the article:
On the encoding and decoding of calcium signals in hepatocytes
Ann Zahle Larsen, Lars Folke Olsen and Ursula Kummera Biophysical ChemistryVolume 107, Issue 1, 1 January 2004, Pages 83-99 14871603,
Abstract:
Many different agonists use calcium as a second messenger. Despite intensive research in intracellular calcium signalling it is an unsolved riddle how the different types of information represented by the different agonists, is encoded using the universal carrier calcium. It is also still not clear how the information encoded is decoded again into the intracellular specific information at the site of enzymes and genes. After the discovery of calcium oscillations, one likely mechanism is that information is encoded in the frequency, amplitude and waveform of the oscillations. This hypothesis has received some experimental support. However, the mechanism of decoding of oscillatory signals is still not known. Here, we study a mechanistic model of calcium oscillations, which is able to reproduce both spiking and bursting calcium oscillations. We use the model to study the decoding of calcium signals on the basis of co-operativity of calcium binding to various proteins. We show that this co-operativity offers a simple way to decode different calcium dynamics into different enzyme activities.

Note:

This model corresponds to the 5 variable receptor-operated model, as described by Larsen et al., 2004. This model is a modified version of the model described in Kummer 2000 (PMID:10968983)

Model
Publication ID: 14871603 Submission Date: 06 May 2011 14:45:33 UTC Last Modification Date: 28 May 2014 02:48:31 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)
Rate Rule (variable: Calcium-mit)      
Physical entities
Compartments Species
cytoplasm G-alpha PLC Calcium-Cyt
     
ER Calcium-ER    
mitochondria Calcium-mit    
Global parameters
k1 k2 k3 K4
k5 K6 k7 k8
K9 k10 K11 k12
k13 k14 K15 k16
K17 k18 K19 k20
K21      
Reactions (0)
Rules (5)
 
 Rate Rule (name: G_alpha) d [ G-alpha] / d t= k1+k2*G_alpha-k3*G_alpha*PLC/(G_alpha+K4)-k5*G_alpha*Ca_cyt/(G_alpha+K6)
 
 Rate Rule (name: PLC) d [ PLC] / d t= k7*G_alpha-k8*PLC/(PLC+K9)
 
 Rate Rule (name: Ca_cyt) d [ Calcium-Cyt] / d t= (Ca_ER-Ca_cyt)*k10*Ca_cyt*PLC^4/(PLC^4+K11^4)+k12*PLC+k13*G_alpha-k14*Ca_cyt/(Ca_cyt+K15)-k16*Ca_cyt/(Ca_cyt+K17)-k18*Ca_cyt^8/(K19^8+Ca_cyt^8)+(Ca_mit-Ca_cyt)*k20*Ca_cyt/(Ca_cyt+K21)
 
 Rate Rule (name: Ca_ER) d [ Calcium-ER] / d t= (-(Ca_ER-Ca_cyt))*k10*Ca_cyt*PLC^4/(PLC^4+K11^4)+k16*Ca_cyt/(Ca_cyt+K17)
 
 Rate Rule (name: Ca_mit) d [ Calcium-mit] / d t= k18*Ca_cyt^8/(K19^8+Ca_cyt^8)-(Ca_mit-Ca_cyt)*k20*Ca_cyt/(Ca_cyt+K21)
 
 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: 10.0
 
 mitochondria Spatial dimensions: 3.0  Compartment size: 1.0
 
 Calcium-mit
Compartment: mitochondria
Initial concentration: 0.0010
 
Global Parameters (21)
 
 k1
Value: 0.35
Constant
 
 k2
Constant
 
 k3
Value: 1.0E-4
Constant
 
 K4
Value: 0.783
Constant
 
 k5
Value: 1.24
Constant
 
 K6
Value: 0.7
Constant
 
 k7
Value: 5.82
Constant
 
 k8
Value: 32.24
Constant
 
 K9
Value: 29.09
Constant
 
 k10
Value: 0.93
Constant
 
 K11
Value: 2.667
Constant
 
 k12
Value: 0.76
Constant
 
 k13
Constant
 
 k14
Value: 149.0
Constant
 
 K15
Value: 0.16
Constant
 
 k16
Value: 20.9
Constant
 
 K17
Value: 0.05
Constant
 
 k18
Value: 79.0
Constant
 
 K19
Value: 2.0
Constant
 
 k20
Value: 1.5
Constant
 
 K21
Value: 1.5
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000330

Curator's comment: (updated: 12 May 2011 12:09:49 BST)

Figure 2 of the reference publication is reproduced. Cytoplasmic Calcium concentration with varying k1 (k1 denotes the level of agonist binding) value. For (a) k1=0.35, (b) k1=0.45 and (c) k1=0.55.

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

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