- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-05-27 16:25:03+12:00
- Desc:
- Adding BG pic
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/b2d/rawfile/5944d0db540729462392a6409bb43f3abe4e5cbf/exposure/exposure_frontpage.rst
About this model
====================
This is a bond-graph model of the metabolism of generic receptor tyrosine kinase (RTK) in the mammalian cell.
**INPUTS:**
- Ligand (L) stimulus
**OUTPUTS:**
- Change in molar amount of phosphorylated RTK K\ :sub:`2`\ P\ :sub:`n`\
**REACTIONS:**
- Re\ :sub:`1`\ : the binding of L to one RTK (K\ :sub:`1`)
- Re\ :sub:`2`\ : formation of complex of two RTK molecules which have dimerized, with ligand present (LK\ :sub:`1` K\ :sub:`2`).
- Re\ :sub:`3`\ : autophosphorylation of RTKs in the dimer.
- Re\ :sub:`4`\ : binding of ubiquitin to resulting ligand-RTK complex
- Re\ :sub:`5`\ : Ubiquitin-tagged complex gets sorted for RTK to be recycled, and other constituents to be degraded.
- Re\ :sub:`6`\ : Ubiquitin-tagged complex gets sorted for RTK to be degraded by hydrolysis inside a lysosome.
Model status
=============
The current CellML implementation runs in OpenCOR.
Model overview
===================
The following model of RTK action is based on what is widely known in literature.
.. figure:: exposure/BG_diagram.png
:width: 100%
:align: center
:alt: BG RTK reaction
Bond-graph formulation of the generic RTK network. E represents the RTK protein. Because this model is generic, :math:`{n}` would change depending on the chosen reaction.
|
.. csv-table:: List of chemical species
:header: "Abbreviation", "Name"
:widths: 5, 15
"K", "Receptor tyrosine kinase (RTK)"
"L", "Ligand"
"P\ :sub:`i`", "Phosphate"
"U", "Ubiquitin"
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/b2d/file/722d3150e09052999ed676cd31c39aa16e20a0bd/parameter_finder/kinetic_parameters_RTK.py>`_.
Here, this solve process is performed in Python.
