Location: Baylor, Hollingworth, Chandler, 2002 @ 090a57d91ae1 / baylor_hollingworth_chandler_2002_b.cellml

Author:
pmr2.import <nobody@models.cellml.org>
Date:
2009-05-05 00:11 +1200
Desc:
committing version03 of baylor_hollingworth_chandler_2002
Permanent Source URI:
http://models.cellml.org/workspace/baylor_hollingworth_chandler_2002/rawfile/090a57d91ae1939d2364aac8a172546fd9df1f9f/baylor_hollingworth_chandler_2002_b.cellml

<?xml version='1.0' encoding='utf-8'?>
<!--  FILE :baylor_model_b_2002_version02.xml

CREATED :  23rd May 2007

LAST MODIFIED : 23rd 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 Baylor, Hollingworth and Chandler's 2002 model of the Ca2+-ATP binding reaction in skeletal myocytes.

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="baylor_model_b_2002_version02" name="baylor_model_f_2002">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
  <articleinfo>
  <title>Calcium Sparks in Skeletal Muscle Fibers</title>
  <author>
    <firstname>Catherine</firstname>
          <surname>Lloyd</surname>

    <affiliation>
      <shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
    </affiliation>
  </author>
</articleinfo>
      <section id="sec_status">
    <title>Model Status</title>
    <para>
            This model is coded according to the description in the publication but is not able to reproduce the published results.
          </para>
<para>
ValidateCellML detects units inconsistencies within this model.
</para>
  </section>
  <sect1 id="sec_structure">
<title>Model Structure</title>

<para>
The activation of Ca<superscript>2+</superscript> sparks is an essential step in cardiac excitation-contraction coupling.  A Ca<superscript>2+</superscript> spark arises when sarcoplasmic reticulum (SR) Ca<superscript>2+</superscript>-release channels (ryanodine receptors, or RyRs) open, allowing Ca<superscript>2+</superscript> to diffuse out of the intracellular store, down its electrochemical gradient into the cytoplasm.  The increase in intracellular calcium concentration ([Ca<superscript>2+</superscript>]<subscript>i</subscript>) is recognised as a Ca<superscript>2+</superscript> spark.  After release, Ca<superscript>2+</superscript> diffuses through the cytoplasm and binds to buffers such as troponin, ATP, parvalbumin and the SR Ca<superscript>2+</superscript> pump. 

</para>

<para>
In their 2002 paper, S.M. Baylor, S. Hollingworth and W.K. Chandler model Ca<superscript>2+</superscript> sparks in frog intact skeletal muscle fibers.  The model calculates changes in the concentration of free Ca<superscript>2+</superscript> and of Ca<superscript>2+</superscript> bound to the buffers and to the Ca<superscript>2+</superscript> indicator fluo-3 (see <xref linkend="fig_reaction_diagram"/> below).   

</para>

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

<para>
<ulink url="http://www.jgp.org/cgi/content/abstract/120/3/349">Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog</ulink>, S.M. Baylor, S. Hollingworth and W.K. Chandler, 2002, <ulink url="http://www.jgp.org/">
            <emphasis>Journal of General Physiology</emphasis>
          </ulink>, 120, 349-368. (<ulink url="http://www.jgp.org/cgi/content/full/120/3/349">Full text</ulink> and <ulink url="http://www.jgp.org/cgi/reprint/120/3/349.pdf">PDF versions</ulink> of the article are available to subscribers on the Journal of General Physiology website.)  <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12198091&amp;dopt=Abstract">PubMed ID: 12198091</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="reaction_diagram.gif"/>
  </imageobject>
</mediaobject>
<caption>Schematic diagrams of the Ca<superscript>2+</superscript> binding reactions for various buffers and indicators: <emphasis role="bold">A</emphasis>  The reaction of Ca<superscript>2+</superscript> with ATP in the presence of free Mg<superscript>2+</superscript>, <emphasis role="bold">B</emphasis>  Reaction of Ca<superscript>2+</superscript> with protein (Pr) and fluo-3 (Fluo), <emphasis role="bold">C</emphasis>  Competitive reaction of Ca<superscript>2+</superscript> and Mg<superscript>2+</superscript> with parvalbumin (Parv), <emphasis role="bold">D</emphasis>  Binding reaction of Ca<superscript>2+</superscript> binding and transport by the sarcoplasmic reticulum Ca<superscript>2+</superscript> pump (E), <emphasis role="bold">E</emphasis>  One-step reaction of Ca<superscript>2+</superscript> with Troponin (Trop), and <emphasis role="bold">F</emphasis>  Two-step reaction of Ca<superscript>2+</superscript> with Troponin (Trop).</caption>

</informalfigure>

</sect1>
</article>
</documentation>
  
    
  
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      <unit units="litre" exponent="-1"/>
   </units>

   <units name="molar">
      <unit units="litre" exponent="-1"/>
   </units>
   
   <units name="first_order_rate_constant">
      <unit units="second" exponent="-1"/>
   </units>
  
   <units name="second_order_rate_constant">
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      <unit units="second" exponent="-1"/>
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   <component name="environment">
      <variable units="second" public_interface="out" name="time"/>
   </component>
   
   
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      <variable units="micromolar" public_interface="in" name="PrFluo"/>
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      <variable units="second_order_rate_constant" public_interface="in" name="k3"/>
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      <map_variables variable_2="k1_" variable_1="k1_"/>
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      <map_variables variable_2="k2_" variable_1="k2_"/>
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      <map_variables variable_2="k4_" variable_1="k4_"/>
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      <map_variables variable_2="k4" variable_1="k4"/>
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<rdf:RDF>
  <rdf:Bag rdf:about="rdf:#469a85be-6bae-442e-8dc9-7d8e343bd297">
    <rdf:li>skeletal muscle</rdf:li>
    <rdf:li>calcium dynamics</rdf:li>
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