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BIOMD0000000145 - Wang2007 - ATP induced intracellular Calcium Oscillation

 

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Reference Publication
Publication ID: 17188305
Wang J, Huang X, Huang W.
A quantitative kinetic model for ATP-induced intracellular Ca2+ oscillations.
J. Theor. Biol. 2007 Apr; 245(3): 510-519
Environmental Science Division, School of Earth and Space Science, University of Science and Technology of China, Hefei, Anhui Province 230026, China.  [more]
Model
Original Model: BIOMD0000000145.origin
Submitter: Harish Dharuri
Submission ID: MODEL8342350003
Submission Date: 03 Sep 2007 10:22:47 UTC
Last Modification Date: 31 Mar 2014 11:58:54 UTC
Creation Date: 28 Aug 2007 14:35:18 UTC
Encoders:  Harish Dharuri
   Vijayalakshmi Chelliah
set #1
bqmodel:isDerivedFrom PubMed 1647879
set #2
bqbiol:hasTaxon Taxonomy cellular organisms
set #3
bqbiol:hasPart KEGG Pathway Calcium signaling pathway - Homo sapiens (human)
Gene Ontology positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway
set #4
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes
Wang2007 - ATP induced intracellular Calicum Oscillation

The model simulate the ATP-induced intracellular Ca2+ oscillations and the quantitative effect of ATP concentration on the oscillation characteristics such as the duration, peak concentration of intracellular Ca2+ and average interval.

This model is described in the article:

Wang J, Huang X, Huang W.
J. Theor. Biol. 2007 Apr; 245(3): 510-519

Abstract:

A quantitative kinetic model is proposed to simulate the ATP-induced intracellular Ca(2+) oscillations. The quantitative effect of ATP concentration upon the oscillations was successfully simulated. Our simulation results support previous experimental explanations that the Ca(2+) oscillations are mainly due to interaction of Ca(2+) release from the endoplasmic reticulum (ER) and the ATP-dependent Ca(2+) pump back into the ER, and the oscillations are prolonged by extracellular Ca(2+) entry that maintains the constant Ca(2+) supplies to its intracellular stores. The model is also able to simulate the sudden disappearance phenomenon of the Ca(2+) oscillations observed in some cell types by taking into account of the biphasic characteristic of the Ca(2+) release from the endoplasmic reticulum (ER). Moreover, the model simulation results for the Ca(2+) oscillations characteristics such as duration, peak [Ca(2+)](cyt), and average interval, etc., lead to prediction of some possible factors responsible for the variations of Ca(2+) oscillations in different types of cells.

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: 17188305 Submission Date: 03 Sep 2007 10:22:47 UTC Last Modification Date: 31 Mar 2014 11:58:54 UTC Creation Date: 28 Aug 2007 14:35:18 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
R9 R10 R11  
Rules
Assignment Rule (variable: Diacylglycerol) Assignment Rule (variable: Raplc) Assignment Rule (variable: Rpkc) Assignment Rule (variable: Rgalpha_gtp)
Assignment Rule (variable: Rdg) Assignment Rule (variable: Rip3) Assignment Rule (variable: Rcyt1) Assignment Rule (variable: Rcyt2)
Assignment Rule (variable: Rer) Assignment Rule (variable: PLC)    
Physical entities
Compartments Species
Cytosol Galpha_GTP APLC IP3
Calcium PLC Diacylglycerol
ER Calcium    
Global parameters
Raplc Kp Rpkc Kd
Kr Rgalpha_gtp n Kg
Rdg m Rip3 Ks
Rcyt1 Kc1 Rcyt2 Kc2
Rer w Ker Cplc_total
k0 k1 k2 k3
k4 k5 k6 k7
k8 k9 k10 k11
Reactions (11)
 
 R1  → [Galpha_GTP];  
 
 R2  → [Galpha_GTP];  
 
 R3 [Galpha_GTP] → ;  
 
 R4 [Galpha_GTP] → ;  
 
 R5  → [APLC];   {PLC}
 
 R6 [APLC] → ;  
 
 R7  → [IP3];   {APLC}
 
 R8 [IP3] → ;  
 
 R9 0.0010 × [Calcium] ↔ 0.01 × [Calcium];  
 
 R10 0.05 × [Calcium] → ;  
 
 R11  → 0.05 × [Calcium];  
 
Rules (10)
 
 Assignment Rule (name: DG) Diacylglycerol = IP3
 
 Assignment Rule (name: Raplc) Raplc = APLC/(Kp+APLC)
 
 Assignment Rule (name: Rpkc) Rpkc = DG/(Kd+DG)*Ca_Cyt/(Kr+Ca_Cyt)
 
 Assignment Rule (name: Rgalpha_gtp) Rgalpha_gtp = Galpha_GTP^n/(Kg^n+Galpha_GTP^n)
 
 Assignment Rule (name: Rdg) Rdg = DG^m/(Kd^m+DG^m)
 
 Assignment Rule (name: Rip3) Rip3 = IP3^3/(Ks^3+IP3^3)
 
 Assignment Rule (name: Rcyt1) Rcyt1 = Ca_Cyt/(Kc1+Ca_Cyt)
 
 Assignment Rule (name: Rcyt2) Rcyt2 = Ca_Cyt/(Kc2+Ca_Cyt)
 
 Assignment Rule (name: Rer) Rer = Ca_ER^w/(Ker^w+Ca_ER^w)
 
 Assignment Rule (name: PLC) PLC = Cplc_total-APLC
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Galpha_GTP
Compartment: Cytosol
Initial concentration: 1.0
 
 APLC
Compartment: Cytosol
Initial concentration: 9.0
 
 IP3
Compartment: Cytosol
Initial concentration: 1.0
 
 Calcium
Compartment: Cytosol
Initial concentration: 200.0
 
  PLC
Compartment: Cytosol
Initial concentration: 1.0
 
  Diacylglycerol
Compartment: Cytosol
Initial concentration: 1.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Calcium
Compartment: ER
Initial concentration: 1000.0
 
Global Parameters (32)
 
   Raplc  
 
   Kp
Value: 4.0
Constant
 
   Rpkc  
 
   Kd
Value: 10.0
Constant
 
   Kr
Value: 200.0
Constant
 
   Rgalpha_gtp  
 
   n
Value: 4.0
Constant
 
   Kg
Value: 25.0
Constant
 
   Rdg  
 
   m
Value: 2.0
Constant
 
   Rip3  
 
   Ks
Value: 25.0
Constant
 
   Rcyt1  
 
   Kc1
Value: 1000.0
Constant
 
   Rcyt2  
 
   Kc2
Value: 2000.0
Constant
 
   Rer  
 
   w
Value: 3.0
Constant
 
   Ker
Value: 75.0
Constant
 
   Cplc_total
Value: 10.0
Constant
 
   k0
Value: 0.1
Constant
 
   k1
Value: 3.4
Constant
 
   k2
Value: 4.0
Constant
 
   k3
Value: 4.5
Constant
 
   k4
Value: 1.2
Constant
 
   k5
Value: 0.12
Constant
 
   k6
Value: 14.0
Constant
 
   k7
Value: 2.0
Constant
 
   k8
Value: 10500.0
Constant
 
   k9
Value: 600.0
Constant
 
   k10
Value: 3000.0
Constant
 
   k11
Value: 260.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000145

Curator's comment: (updated: 31 Mar 2014 12:44:42 BST)

Figure 2A of the reference publication has been reproduced here. The simulation was carried out using Copasi v4.11 (Build 64). The plot was generated using Gnuplot.

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