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BIOMD0000000057 - Sneyd2002_IP3_Receptor

  
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Reference Publication
Publication ID: 11842185
Sneyd J, Dufour JF.
A dynamic model of the type-2 inositol trisphosphate receptor.
Proc. Natl. Acad. Sci. U.S.A. 2002 Feb; 99(4): 2398-2403
Institute of Information and Mathematical Sciences, Massey University, Albany Campus, Private Bag 102-904, North Shore Mail Centre, Auckland, New Zealand. jsneyd@massey.ac.nz  [more]
Model
Original Model: BIOMD0000000057.origin
Submitter: Harish Dharuri
Submission ID: MODEL9098147664
Submission Date: 08 Jun 2006 08:05:15 UTC
Last Modification Date: 24 Feb 2015 20:32:18 UTC
Creation Date: 30 May 2006 12:07:25 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf Gene Ontology calcium-mediated signaling
Gene Ontology inositol phosphate-mediated signaling
bqbiol:is KEGG Pathway Calcium signaling pathway
bqbiol:hasTaxon Taxonomy Rattus rattus
Notes

This model was successfully tested on Jarnac and MathSBML. The model reproduces the time profile of "Open Probability" of the receptor as shown in Figure 4 of the publication. The value of calcium ion concentration "c" in this model is 10 microM.


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: 11842185 Submission Date: 08 Jun 2006 08:05:15 UTC Last Modification Date: 24 Feb 2015 20:32:18 UTC Creation Date: 30 May 2006 12:07:25 UTC
Mathematical expressions
Reactions
Receptor-Open state transition Receptor-Inactivated state 1 transition Open-Shut state transition Open-Activated state transition
Activated-Inactivated state 2 transition      
Rules
Assignment Rule (variable: open_probability) Assignment Rule (variable: Phi1) Assignment Rule (variable: Phi2) Assignment Rule (variable: Phi_minus2)
Assignment Rule (variable: Phi3) Assignment Rule (variable: Phi4) Assignment Rule (variable: Phi_minus4) Assignment Rule (variable: Phi5)
Physical entities
Compartments Species
compartment Receptor Open State Inactivated State 1
Shut State Activated State Inactivated State 2
Global parameters
open_probability Phi1 k1 L1
l2 lminus2 c L3
Phi2 k2 l4 Phi_minus2
kminus1 kminus2 kminus3 lminus4
L5 Phi3 k3 Phi4
k4 l6 Phi_minus4 kminus4
lminus6 Phi5 IP3  
Reactions (5)
 
 Receptor-Open state transition [Receptor] ↔ [Open State];  
 
 Receptor-Inactivated state 1 transition [Receptor] ↔ [Inactivated State 1];  
 
 Open-Shut state transition [Open State] ↔ [Shut State];  
 
 Open-Activated state transition [Open State] ↔ [Activated State];  
 
 Activated-Inactivated state 2 transition [Activated State] ↔ [Inactivated State 2];  
 
Rules (8)
 
 Assignment Rule (name: open_probability) open_probability = (0.1*O+0.9*A)^4
 
 Assignment Rule (name: Phi1) Phi1 = (k1*L1+l2)*c/(L1+c*(1+L1/L3))
 
 Assignment Rule (name: Phi2) Phi2 = (k2*L3+l4*c)/(L3+c*(1+L3/L1))
 
 Assignment Rule (name: Phi_minus2) Phi_minus2 = (kminus2+lminus4*c)/(1+c/L5)
 
 Assignment Rule (name: Phi3) Phi3 = k3*L5/(L5+c)
 
 Assignment Rule (name: Phi4) Phi4 = (k4*L5+l6)*c/(L5+c)
 
 Assignment Rule (name: Phi_minus4) Phi_minus4 = L1*(kminus4+lminus6)/(L1+c)
 
 Assignment Rule (name: Phi5) Phi5 = (k1*L1+l2)*c/(L1+c)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Receptor
Compartment: compartment
Initial concentration: 1.0
 
 Open State
Compartment: compartment
Initial concentration: 0.0
 
 Inactivated State 1
Compartment: compartment
Initial concentration: 0.0
 
 Shut State
Compartment: compartment
Initial concentration: 0.0
 
 Activated State
Compartment: compartment
Initial concentration: 0.0
 
 Inactivated State 2
Compartment: compartment
Initial concentration: 0.0
 
Global Parameters (27)
 
   open_probability  
 
   Phi1  
 
   k1
Value: 0.64
Constant
 
   L1
Value: 0.12
Constant
 
   l2
Value: 1.7
Constant
 
   lminus2
Value: 0.8
Constant
 
   c
Value: 10.0
Constant
 
   L3
Value: 0.025
Constant
 
   Phi2  
 
   k2
Value: 37.4
Constant
 
   l4
Value: 1.7
Constant
 
   Phi_minus2  
 
   kminus1
Value: 0.04
Constant
 
   kminus2
Value: 1.4
Constant
 
   kminus3
Value: 29.8
Constant
 
   lminus4
Value: 2.5
Constant
 
   L5
Value: 54.7
Constant
 
   Phi3  
 
   k3
Value: 0.11
Constant
 
   Phi4  
 
   k4
Value: 4.0
Constant
 
   l6
Value: 4707.0
Constant
 
   Phi_minus4  
 
   kminus4
Value: 0.54
Constant
 
   lminus6
Value: 11.4
Constant
 
   Phi5  
 
   IP3
Value: 10.0
Constant
 
Receptor-Open state transition (1)
 
   IP3
Value: 10.0
Constant
 
Receptor-Inactivated state 1 transition (2)
 
   kminus1
Value: 0.04
Constant
 
   lminus2
Value: 0.8
Constant
 
Open-Shut state transition (1)
 
   kminus3
Value: 29.8
Constant
 
Activated-Inactivated state 2 transition (2)
 
   kminus1
Value: 0.04
Constant
 
   lminus2
Value: 0.8
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000057

Curator's comment: (updated: 18 Dec 2006 22:37:15 GMT)

Time profile of Open probability of the IP3 receptor as shown in Fig 4 of the paper. The plot corresponds to a calcium ion concentration of 10 microMolars. Simulation result from Jarnac.
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