The SLC family: NCE (SLC8A1)
======================================================================================

Sodium calcium exchanger

This transporter allows entry of 3 sodium ions, in exchange for the extrusion of one calcium ion. The bond-graph model is illustrated in the figure below, with the CellML model added for simulation purposes.

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

   The bond graph representation of the NCE, 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.


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

.. figure:: alphafold_NCE2.png
   :width: 75%
   :align: center
   :alt: NCE_protein

   NCE 2 structure predicted by Alphafold software: 

*Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).*

*Varadi, M et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research (2024).*
   
Subfamilies
===================
The following list contains all known member of the SLC8 family.

.. csv-table:: Variants within the human species
   :header: "Name", "Alias", Gene, Structure
   :widths: 7,7,7,7
   
   SLC8A1, NCE1/NAC1, `Uniprot 1 <https://www.uniprot.org/uniprotkb/P32418/entry>`_, `PDB 1 <https://www.ebi.ac.uk/pdbe-srv/view/entry/8JP0>`_
   SLC8A2, NCE2/NAC2, `Uniprot 2 <https://www.uniprot.org/uniprotkb/Q9UPR5/entry>`_, `Alphafold 2 <https://alphafold.ebi.ac.uk/entry/Q9UPR5>`_
   SLC8A3, NCE3/NAC3, `Uniprot 3 <https://www.uniprot.org/uniprotkb/P57103/entry>`_, `Alphafold 3 <https://alphafold.ebi.ac.uk/entry/P57103>`_


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_NCE <https://models.physiomeproject.org/workspace/828>`_", "S Fong" 
   "`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."
   "`IPSC-model <https://github.com/ClancyLabUCD/IPSC-model>`_", "Kernik et al."

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


Other annotations
===================

.. csv-table:: 
   :header: "Item", "Database"
   :widths: 17, 15
   
   "calcium:sodium antiporter activity", "`Gene Ontology <https://amigo.geneontology.org/amigo/term/GO:0005432>`_"


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