- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-05-02 13:25:40+12:00
- Desc:
- delete sentence
- Permanent Source URI:
- https://models.cellml.org/workspace/848/rawfile/98c2d94ee9d4dbdfcd74f4bc2dde0c8eeb9e61a5/exposure/exposure_frontpage.rst
About this model
====================
This is a bond-graph model of the metabolism of the phospholipase-C beta variant (PLC) and the associated Gq protein in the mammalian cell.
**INPUTS:**
- Gq protein (Gq)
**OUTPUTS:**
- Change in molar amount of diacylglycerol (DAG), inositol trisphosphate (IP3), calcium (Ca)
**REACTIONS:**
- R0: Conversion of DAG into phosphatidylcholine (PC)
- R1: Conversion of IP3 into inositol (Ino)
- R2: PLC complex CaPLC catalysing the splitting of phosphatidylinositol biphosphate (PIP2) into DAG and IP3
- R3: Similar to R2, but with enzyme complex CaGqPLC
- R4: Binding of Ca and PLC
- R5: Binding of Gq and PLC
- R6: Binding of Ca and GqPLC
- R7: Unbinding of Gq from CaGqPLC
- R8: Unbinding of Gq (in G*GDP form) from CaGqPLC
Model status
=============
The current CellML implementation runs in OpenCOR.
Model overview
===================
This model is based on existing kinetic model, where the mathematics are translated into the bond-graph formalism. This describes the model in energetic terms and forces adherence to the laws of thermodynamics.
.. figure:: exposure/BG_PLC.png
:width: 100%
:align: center
:alt: BG PLC reaction
Fig. 1. Bond-graph formulation of the PLC network
|
For the above bond-graphs, a '0' node refers to a junction where all chemical potentials are the same. A '1' node refers to all fluxes being the same going in and out of the junction.
.. csv-table:: List of chemical species
:header: "Abbreviation", "Name"
:widths: 5, 15
"PLC", "Phospholipase-C (beta variant)"
"Ca", "Calcium ion"
"Gq", "Gq protein"
"DAG", "Diacylglycerol"
"IP3", "Inositol trisphosphate"
"Ino", "Inositol"
"PIP2", "Phosphatidylinositol biphosphate"
"PC", "Phosphatidylcholine"
Parameter finding
~~~~~~~~~~~~~~~~~
A description of the process to find bond-graph parameters is shown in the folder `parameter_finder <parameter_finder>`_, which relies on the:
1. stoichiometry of system
2. kinetic constants for forward/reverse reactions
- If not already, all reactions are made reversible by assigning a small value to the reverse direction.
3. `linear algebra script <https://models.physiomeproject.org/workspace/848/rawfile/6239317b4238524d2bf82a54c50849558a4d67d7/parameter_finder/kinetic_parameters_PLC.py>`_.
Here, this solve process is performed in Python.
Original kinetic model
======================
Bhalla and Iyengar: `Emergent properties of networks of biological signaling pathways. <https://models.physiomeproject.org/e/7e3>`_
