Rendering of the source text

<?xml version='1.0' encoding='utf-8'?>
<!--  FILE :nagerl_model_2000.xml

CREATED :  22nd May 2007

LAST MODIFIED : 22nd May 2007

AUTHOR :  Catherine Lloyd
          Bioengineering Institute
          The University of Auckland
          
MODEL STATUS :  This model conforms to the CellML 1.1 Specification.

DESCRIPTION :  This file contains a CellML description of Nagerl et al's 2000 study of the binding kinetics of calbindin-D28k.

CHANGES:  
  
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="nagerl_model_2000_version02" name="nagerl_novo_mody_vergara_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
  <articleinfo>
  <title>Ca2+ Binding Kinetics of Calbindin-D28k</title>
  <author>
    <firstname>Catherine</firstname>
          <surname>Lloyd</surname>
    <affiliation>
      <shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
    </affiliation>
  </author>
</articleinfo>
  <sect1 id="sec_structure">
<title>Model Structure</title>

<para>
Rapid changes in intracellular calcium concentration ([Ca<superscript>2+</superscript>]<subscript>i</subscript>) are characteristic of Ca<superscript>2+</superscript> signalling.  Following a stimulus, Ca<superscript>2+</superscript> flows into the cytoplasm through channels in the cell membrane, and it's released from intracellular stores such as the endoplasmic reticulum.  Normal [Ca<superscript>2+</superscript>] is resumed by the actions of Ca<superscript>2+</superscript> pumps, exchangers, binding proteins (CBPs) and other buffers.  Calbindin-D<subscript>28k</subscript> is a CBP which is present at high cytosolic concentrations in neurons such as cerebellar Purkinje cells and hippocampal granule cells.  Together with its high cytosolic concentration, the ability of calbindin-D<subscript>28k</subscript> to bind up to four Ca<superscript>2+</superscript> ions at any one time suggests that it plays an important role in Ca<superscript>2+</superscript> buffering. 
</para>

<para>
Little is known about the Ca<superscript>2+</superscript> binding kinetics of calbindin-D<subscript>28k</subscript>, or of CBPs in general.  In their 2000 paper, Nagerl <emphasis>et al.</emphasis> describe a new method to measure the binding kinetics of calbindin-D<subscript>28k</subscript>, which involves flash photolysis of DM-nitrophen (DM-n), a caged Ca<superscript>2+</superscript> compound.  A mathematical model, which included the Ca<superscript>2+</superscript> binding reactions of all the species in the solution (see <xref linkend="fig_reaction_diagram"/> below), was fitted to the experimental data in order to determine realistic kinetic parameters.  The results of their experiments suggested that calbindin-D<subscript>28k</subscript> has two kinetically distinct types of Ca<superscript>2+</superscript> binding sites, one high- and one low-affinity.  This heterogeneity was captured by their mathematical model.   
</para>

<para>
The complete original paper reference is cited below:
</para>

<para>
<ulink url="http://www.biophysj.org/cgi/content/abstract/79/6/3009">Binding Kinetics of Calbindin-D<subscript>28k</subscript> Determined by Flash Photolysis of Caged Ca<superscript>2+</superscript>
          </ulink>, U. Valentin Nagerl, David Novo, Istvan Mody and Julio L. Vergara, 2000, <ulink url="http://www.biophysj.org/">
            <emphasis>Biophysical Journal</emphasis>
          </ulink>, 79, 3009-3018. (<ulink url="http://www.biophysj.org/cgi/content/full/79/6/3009">Full text</ulink> and <ulink url="http://www.biophysj.org/cgi/reprint/79/6/3009.pdf">PDF versions</ulink> of the article are available to subscribers on the Biophysical Journal website.)  <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=11106608&amp;dopt=Abstract">PubMed ID: 11106608</ulink> 
</para>

<para>
The raw CellML descriptions of the model can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>.
</para>

<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
  <imageobject>
    <objectinfo>
      <title>reaction_diagram</title>
    </objectinfo>
    <imagedata fileref="nagerl_2000.png"/>
  </imageobject>
</mediaobject>
<caption>Schematic diagram of the mathematical model used to simulate the dynamic redistribution of Ca<superscript>2+</superscript> generated by flash photolysis of DM-n.  CaDM1, CaDM2, CaD and CaB represent the concentration of Ca<superscript>2+</superscript> bound to DM-n, dye and buffer, respectively.  Alpha models the fraction of Ca<superscript>2+</superscript>-bound DM-n1 that is photolysed by the UV laser flash.</caption>
</informalfigure>

</sect1>
</article>
</documentation>




  
    
  
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   <units name="millisecond">
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      <variable units="micromolar" public_interface="in" name="Ca"/>
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     <variable units="millisecond" public_interface="in" name="time"/>

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  `
  
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      <map_variables variable_2="CaD" variable_1="CaD"/>
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      <map_variables variable_2="CaBi" variable_1="CaBi"/>
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   <connection>
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        Nagerl et al's 2000 study of the binding kinetics of calbindin-D28k.
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    <dc:title>Binding Kinetics of Calbindin-D28k Determined by Flash Photolysis of Caged Ca2+</dc:title>
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    <dc:title>Biophysical Journal</dc:title>
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    <dcterms:W3CDTF>2007-05-22</dcterms:W3CDTF>
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    <vCard:Given>Catherine</vCard:Given>
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    <vCard:Given>David</vCard:Given>
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