ATPase pumps: Calcium ATPase (SERCA)
======================================================================================

This ATPase pumps out 2 calcium ions from the sarcoplasmic reticulum, and one hydrogen ion enters. For this process, one ATP molecule is hydrolysed. The bond-graph model is illustrated in the figure below, with the CellML model added for simulation purposes.

.. figure::  SERCA_BG_diagram_simplification.png
   :width: 95%
   :align: center
   :alt: Schematic and bond graph of the model

   The bond graph representation of the SERCA, showing simplification of the full bond graph into the reduced form.


Because this has not been parameterised yet, there are no simulation results to show. The associated CellML file contains all equations needed to execute this model.


.. _CellML: https://www.cellml.org/
.. _OpenCOR: https://opencor.ws/
.. _SED-ML: https://sed-ml.org


Protein knowledge
===================

.. figure:: ATP2A1.png
   :width: 50%
   :align: center
   :alt: serca_pic

   Fig. 1. Structure of the ATP2A1 protein, rendered from PDB structure

Subfamilies
===================
The following list contains the known subfamilies of SERCA pump.

.. csv-table:: Variants within the human species
   :header: "Channel name", "Alias", Gene, Structure
   :widths: 7,7,7,7
   
   SERCA1, ATP2A1, `Uniprot 1 <https://www.uniprot.org/uniprotkb/O14983/entry>`_, `SMR 1 <https://swissmodel.expasy.org/repository/uniprot/O14983?csm=C8F33809B56FDDEE>`_
   SERCA2, ATP2A2, `Uniprot 2 <https://www.uniprot.org/uniprotkb/P16615/entry>`_, `PDB 2 <https://www.ebi.ac.uk/pdbe-srv/view/entry/5ZTF>`_
   SERCA3, ATP2A3, `Uniprot 3 <https://www.uniprot.org/uniprotkb/Q93084/entry>`_, `SMR 3 <https://swissmodel.expasy.org/repository/uniprot/Q93084?csm=44E9F1FBF41FE36A>`_



Literature
===================

.. csv-table:: For further reading
   :header: "Title", "Author"
   :widths: 30, 15   
   
   "`A computational model of induced pluripotent stem-cell derived cardiomyocytes incorporating experimental variability from multiple data sources <https://doi.org/10.1113/JP278739>`_", "Kernik et al."
   "`A thermodynamic framework for modelling membrane transporters <https://arxiv.org/abs/1806.04341>`_", "Pan et al."

Existing models 
===================

.. csv-table:: Link to other PMR workspaces or exposures
   :header: "Title", "Author"
   :widths: 30, 15
   
   "`BG_SERCA <https://models.physiomeproject.org/workspace/7a5>`_", "S Fong" 
   "`Transporter_thermodynamics^ <https://github.com/uomsystemsbiology/transporter_thermodynamics>`_", "Pan et al."
   "`Bond graph modelling of the cardiac action potential: Implications for drift and non-unique steady states <https://github.com/uomsystemsbiology/bond_graph_cardiac_AP>`_", "M Pan et al."
   "`A Thermodynamic Model of the Cardiac Sarcoplasmic/Endoplasmic Ca(2+) (SERCA) Pump: the three-state SERCA model* <https://models.physiomeproject.org/exposure/d3bde1a45f3b2778875a6a446618e336/tran_smith_loiselle_crampin_2009.cellml/view>`_", "Tran et al."

   
Models denoted by [*] are not in bond graph form.
Models denoted by [^] are part of a whole cell model.