Sneyd2002_IP3_Receptor

  public model
Model Identifier
BIOMD0000000057
Short description

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.


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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.

Format
SBML (L2V1)
Related Publication
  • A dynamic model of the type-2 inositol trisphosphate receptor.
  • Sneyd J, Dufour JF
  • Proceedings of the National Academy of Sciences of the United States of America , 2/ 2002 , Volume 99 , pages: 2398-2403 , PubMed ID: 11842185
  • 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
  • The dynamic properties of the inositol (1,4,5)-trisphosphate (IP(3)) receptor are crucial for the control of intracellular Ca(2+), including the generation of Ca(2+) oscillations and waves. However, many models of this receptor do not agree with recent experimental data on the dynamic responses of the receptor. We construct a model of the IP(3) receptor and fit the model to dynamic and steady-state experimental data from type-2 IP(3) receptors. Our results indicate that, (i) Ca(2+) binds to the receptor using saturating, not mass-action, kinetics; (ii) Ca(2+) decreases the rate of IP(3) binding while simultaneously increasing the steady-state sensitivity of the receptor to IP(3); (iii) the rate of Ca(2+)-induced receptor activation increases with Ca(2+) and is faster than Ca(2+)-induced receptor inactivation; and (iv) IP(3) receptors are sequentially activated and inactivated by Ca(2+) even when IP(3) is bound. Our results emphasize that measurement of steady-state properties alone is insufficient to characterize the functional properties of the receptor.
Contributors
Harish Dharuri

Metadata information

is
BioModels Database MODEL9098147664
BioModels Database BIOMD0000000057
KEGG Pathway Calcium signaling pathway
isDescribedBy
PubMed 11842185
hasTaxon
Taxonomy Rattus rattus
isVersionOf

Curation status
Curated

Tags
Name Description Size Actions

Model files

BIOMD0000000057_url.xml SBML L2V1 representation of Sneyd2002_IP3_Receptor 26.60 KB Preview | Download

Additional files

BIOMD0000000057-biopax3.owl Auto-generated BioPAX (Level 3) 14.96 KB Preview | Download
BIOMD0000000057_urn.xml Auto-generated SBML file with URNs 26.05 KB Preview | Download
BIOMD0000000057.xpp Auto-generated XPP file 4.61 KB Preview | Download
BIOMD0000000057.sci Auto-generated Scilab file 3.88 KB Preview | Download
BIOMD0000000057.pdf Auto-generated PDF file 163.69 KB Preview | Download
BIOMD0000000057.m Auto-generated Octave file 6.87 KB Preview | Download
BIOMD0000000057.png Auto-generated Reaction graph (PNG) 23.64 KB Preview | Download
BIOMD0000000057-biopax2.owl Auto-generated BioPAX (Level 2) 10.63 KB Preview | Download
BIOMD0000000057.svg Auto-generated Reaction graph (SVG) 12.63 KB Preview | Download
BIOMD0000000057.vcml Auto-generated VCML file 24.40 KB Preview | Download

  • Model originally submitted by : Harish Dharuri
  • Submitted: Jun 8, 2006 9:05:15 AM
  • Last Modified: Feb 24, 2015 8:32:18 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Feb 24, 2015 8:32:18 PM
    • Submitted by: Harish Dharuri
    • With comment: Current version of Sneyd2002_IP3_Receptor
  • Version: 1 public model Download this version
    • Submitted on: Jun 8, 2006 9:05:15 AM
    • Submitted by: Harish Dharuri
    • With comment: Original import of Sneyd2002_IP3_Receptor

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
I2

IPR000493
0.0 μmol
R

IPR000493
1.0 μmol
O

IPR000493
0.0 μmol
S

IPR000493
0.0 μmol
A

IPR000493
0.0 μmol
I1

IPR000493
0.0 μmol
Reactions
Reactions Rate Parameters
A => I2 compartment*(Phi5*A-(kminus1+lminus2)*I2) lminus2 = 0.8; kminus1 = 0.04; lminus2=0.8; kminus1=0.04; Phi5 = 0.0
R => I1 compartment*(Phi1*R-(kminus1+lminus2)*I1) lminus2 = 0.8; kminus1 = 0.04; Phi1 = 0.0; lminus2=0.8; kminus1=0.04
R => O compartment*(Phi2*IP3*R-Phi_minus2*O) IP3=10.0; IP3 = 10.0; Phi_minus2 = 0.0; Phi2 = 0.0
O => S compartment*(Phi3*O-kminus3*S) kminus3 = 29.8; kminus3=29.8; Phi3 = 0.0
O => A compartment*(Phi4*O-Phi_minus4*A) Phi4 = 0.0; Phi_minus4 = 0.0
Curator's comment:
(added: 18 Dec 2006, 22:37:15, updated: 18 Dec 2006, 22:37:15)
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.