Location: Baylor, Hollingworth, Chandler, 2002 @ d68623da04e6 / baylor_hollingworth_chandler_2002_b.cellml

Author:
pmr2.import <nobody@models.cellml.org>
Date:
2007-05-18 05:44:35+12:00
Desc:
committing version01 of baylor_hollingworth_chandler_2002
Permanent Source URI:
http://models.cellml.org/workspace/baylor_hollingworth_chandler_2002/rawfile/d68623da04e6a3aae359999f6d50e57c3d729523/baylor_hollingworth_chandler_2002_b.cellml

<?xml version='1.0' encoding='utf-8'?>
<!--  FILE :baylor_model_b_2002.xml

CREATED :  1st November 2002

LAST MODIFIED : 9th April 2003

AUTHOR :  Catherine Lloyd
          Bioengineering Institute
          The University of Auckland
          
MODEL STATUS :  This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/01/2002 CellML Metadata 1.0 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:  
  09/04/2003 - AAC - Added publication date information.  

--><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#" name="baylor_model_b_2002" cmeta:id="baylor_model_b_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 is the original unchecked version of the model imported from the previous
            CellML model repository, 24-Jan-2006.
          </para>
    <para>
        This model describes Multistate reaction of Ca2+ and protein with fluo-3
    </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>

  
    
  <!--
    Below, we define some additional units for association with variables and
    constants within the model. The identifiers are fairly self-explanatory.
  -->

   <units name="micromolar">
      <unit units="mole" prefix="micro"/>
      <unit units="litre" exponent="-1"/>
   </units>
   
   <units name="molar">
      <unit units="litre" exponent="-1"/>
   </units>
   
   <units name="flux">
      <unit units="micromolar" exponent="1"/>
      <unit units="second" exponent="-1"/>
   </units>
   
   <units name="first_order_rate_constant">
      <unit units="second" exponent="-1"/>
   </units>
  
   <units name="second_order_rate_constant">
      <unit units="molar" exponent="-1"/>
      <unit units="second" exponent="-1"/>
   </units>
  
  <!--
    The "environment" component is used to declare variables that are used by
    all or most of the other components, in this case just "time".
  -->
   
   <component name="environment">
      <variable units="second" public_interface="out" name="time"/>
   </component>
   
   <!--
    The following components describe all the reactants and products involved in
    the reactions. 
   --> 
   
   <component cmeta:id="Ca" name="Ca">
      <variable units="micromolar" public_interface="out" name="Ca" initial_value="0.05"/>
      <variable units="flux" public_interface="in" name="delta_Ca_rxn0"/>
      <variable units="flux" public_interface="in" name="delta_Ca_rxn3"/>
      <variable units="second" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Ca</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Ca_rxn0</ci>
               <ci>delta_Ca_rxn3</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Fluo" name="Fluo">
      <variable units="micromolar" public_interface="out" name="Fluo" initial_value="11.88"/>
      <variable units="flux" public_interface="in" name="delta_Fluo_rxn0"/>
      <variable units="flux" public_interface="in" name="delta_Fluo_rxn1"/>
      <variable units="second" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Fluo</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Fluo_rxn0</ci>
               <ci>delta_Fluo_rxn1</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Pr" name="Pr">
      <variable units="micromolar" public_interface="out" name="Pr" initial_value="3000.0"/>
      <variable units="flux" public_interface="in" name="delta_Pr_rxn1"/>
      <variable units="flux" public_interface="in" name="delta_Pr_rxn2"/>
      <variable units="second" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Pr</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Pr_rxn1</ci>
               <ci>delta_Pr_rxn2</ci>
            </apply>
         </apply>
      </math>
   </component>
  
   <component cmeta:id="PrFluo" name="PrFluo">
      <variable units="micromolar" public_interface="out" name="PrFluo" initial_value="88.12"/>
      <variable units="flux" public_interface="in" name="delta_PrFluo_rxn1"/>
      <variable units="flux" public_interface="in" name="delta_PrFluo_rxn3"/>
      <variable units="second" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>PrFluo</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_PrFluo_rxn1</ci>
               <ci>delta_PrFluo_rxn3</ci>
            </apply>
         </apply>
      </math>
   </component>
  
   <component cmeta:id="CaFluo" name="CaFluo">
      <variable units="micromolar" public_interface="out" name="CaFluo"/>
      <variable units="flux" public_interface="in" name="delta_CaFluo_rxn0"/>
      <variable units="flux" public_interface="in" name="delta_CaFluo_rxn2"/>
      <variable units="second" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>CaFluo</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_CaFluo_rxn0</ci>
               <ci>delta_CaFluo_rxn2</ci>
            </apply>
         </apply>
      </math>
   </component>
  
   <component cmeta:id="CaPrFluo" name="CaPrFluo">
      <variable units="micromolar" public_interface="out" name="CaPrFluo"/>
      <variable units="flux" public_interface="in" name="delta_CaPrFluo_rxn2"/>
      <variable units="flux" public_interface="in" name="delta_CaPrFluo_rxn3"/>
      <variable units="second" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>CaPrFluo</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_CaPrFluo_rxn2</ci>
               <ci>delta_CaPrFluo_rxn3</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <!--
    The following components describe the reactions of the model.
   -->
   
   <component name="reaction0">
      <variable units="micromolar" public_interface="in" name="Ca"/>
      <variable units="micromolar" public_interface="in" name="Fluo"/>
      <variable units="micromolar" public_interface="in" name="CaFluo"/>
      <variable units="flux" public_interface="out" name="delta_Ca_rxn0"/>
      <variable units="flux" public_interface="out" name="delta_Fluo_rxn0"/>
      <variable units="flux" public_interface="out" name="delta_CaFluo_rxn0"/>
      <variable units="second_order_rate_constant" name="k0" initial_value="2.676E8"/>
      <variable units="first_order_rate_constant" name="k0_" initial_value="137.0"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="yes">
         <variable_ref variable="Ca">
            <role role="reactant" direction="forward" delta_variable="delta_Ca_rxn0" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="Fluo">
            <role role="reactant" direction="forward" delta_variable="delta_Fluo_rxn0" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="CaFluo">
            <role role="product" direction="forward" delta_variable="delta_CaFluo_rxn0" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <plus/>
                        <apply>
                           <times/>
                           <ci>k0</ci>
                           <ci>Ca</ci>
                           <ci>Fluo</ci>
                        </apply>
                        <apply>
                           <minus/>
                           <apply>
                              <times/>
                              <ci>k0_</ci>
                              <ci>CaFluo</ci>
                           </apply>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
  
   <component name="reaction1">
      <variable units="micromolar" public_interface="in" name="Fluo"/>
      <variable units="micromolar" public_interface="in" name="Pr"/>
      <variable units="micromolar" public_interface="in" name="PrFluo"/>
      <variable units="flux" public_interface="out" name="delta_Fluo_rxn1"/>
      <variable units="flux" public_interface="out" name="delta_Pr_rxn1"/>
      <variable units="flux" public_interface="out" name="delta_PrFluo_rxn1"/>
      <variable units="second_order_rate_constant" name="k1" initial_value="1.149E7"/>
      <variable units="first_order_rate_constant" name="k1_" initial_value="4216.0"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="yes">
         <variable_ref variable="Fluo">
            <role role="reactant" direction="forward" delta_variable="delta_Fluo_rxn1" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="Pr">
            <role role="reactant" direction="forward" delta_variable="delta_Pr_rxn1" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="PrFluo">
            <role role="product" direction="forward" delta_variable="delta_PrFluo_rxn1" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <plus/>
                        <apply>
                           <times/>
                           <ci>k1</ci>
                           <ci>Fluo</ci>
                           <ci>Pr</ci>
                        </apply>
                        <apply>
                           <minus/>
                           <apply>
                              <times/>
                              <ci>k1_</ci>
                              <ci>PrFluo</ci>
                           </apply>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
   
   <component name="reaction2">
      <variable units="micromolar" public_interface="in" name="CaFluo"/>
      <variable units="micromolar" public_interface="in" name="Pr"/>
      <variable units="micromolar" public_interface="in" name="CaPrFluo"/>
      <variable units="flux" public_interface="out" name="delta_CaFluo_rxn2"/>
      <variable units="flux" public_interface="out" name="delta_Pr_rxn2"/>
      <variable units="flux" public_interface="out" name="delta_CaPrFluo_rxn2"/>
      <variable units="second_order_rate_constant" name="k2" initial_value="1.149E7"/>
      <variable units="first_order_rate_constant" name="k2_" initial_value="15777.0"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="yes">
         <variable_ref variable="CaFluo">
            <role role="reactant" direction="forward" delta_variable="delta_CaFluo_rxn2" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="Pr">
            <role role="reactant" direction="forward" delta_variable="delta_Pr_rxn2" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="CaPrFluo">
            <role role="product" direction="forward" delta_variable="delta_CaPrFluo_rxn2" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <plus/>
                        <apply>
                           <times/>
                           <ci>k2</ci>
                           <ci>CaFluo</ci>
                           <ci>Pr</ci>
                        </apply>
                        <apply>
                           <minus/>
                           <apply>
                              <times/>
                              <ci>k2_</ci>
                              <ci>CaPrFluo</ci>
                           </apply>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
  
   <component name="reaction3">
      <variable units="micromolar" public_interface="in" name="Ca"/>
      <variable units="micromolar" public_interface="in" name="PrFluo"/>
      <variable units="micromolar" public_interface="in" name="CaPrFluo"/>
      <variable units="flux" public_interface="out" name="delta_Ca_rxn3"/>
      <variable units="flux" public_interface="out" name="delta_PrFluo_rxn3"/>
      <variable units="flux" public_interface="out" name="delta_CaPrFluo_rxn3"/>
      <variable units="second_order_rate_constant" name="k3" initial_value="1.72E7"/>
      <variable units="first_order_rate_constant" name="k3_" initial_value="32.9"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="yes">
         <variable_ref variable="Ca">
            <role role="reactant" direction="forward" delta_variable="delta_Ca_rxn3" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="PrFluo">
            <role role="reactant" direction="forward" delta_variable="delta_PrFluo_rxn3" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="CaPrFluo">
            <role role="product" direction="forward" delta_variable="delta_CaPrFluo_rxn3" stoichiometry="1"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <plus/>
                        <apply>
                           <times/>
                           <ci>k3</ci>
                           <ci>Ca</ci>
                           <ci>PrFluo</ci>
                        </apply>
                        <apply>
                           <minus/>
                           <apply>
                              <times/>
                              <ci>k3_</ci>
                              <ci>CaPrFluo</ci>
                           </apply>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
 
   <connection>
      <map_components component_2="reaction0" component_1="Ca"/>
      <map_variables variable_2="Ca" variable_1="Ca"/>
      <map_variables variable_2="delta_Ca_rxn0" variable_1="delta_Ca_rxn0"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction3" component_1="Ca"/>
      <map_variables variable_2="Ca" variable_1="Ca"/>
      <map_variables variable_2="delta_Ca_rxn3" variable_1="delta_Ca_rxn3"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction0" component_1="Fluo"/>
      <map_variables variable_2="Fluo" variable_1="Fluo"/>
      <map_variables variable_2="delta_Fluo_rxn0" variable_1="delta_Fluo_rxn0"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction1" component_1="Fluo"/>
      <map_variables variable_2="Fluo" variable_1="Fluo"/>
      <map_variables variable_2="delta_Fluo_rxn1" variable_1="delta_Fluo_rxn1"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction1" component_1="Pr"/>
      <map_variables variable_2="Pr" variable_1="Pr"/>
      <map_variables variable_2="delta_Pr_rxn1" variable_1="delta_Pr_rxn1"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction2" component_1="Pr"/>
      <map_variables variable_2="Pr" variable_1="Pr"/>
      <map_variables variable_2="delta_Pr_rxn2" variable_1="delta_Pr_rxn2"/>
   </connection>
   
   <connection>
      <map_components component_2="reaction1" component_1="PrFluo"/>
      <map_variables variable_2="PrFluo" variable_1="PrFluo"/>
      <map_variables variable_2="delta_PrFluo_rxn1" variable_1="delta_PrFluo_rxn1"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction3" component_1="PrFluo"/>
      <map_variables variable_2="PrFluo" variable_1="PrFluo"/>
      <map_variables variable_2="delta_PrFluo_rxn3" variable_1="delta_PrFluo_rxn3"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction0" component_1="CaFluo"/>
      <map_variables variable_2="CaFluo" variable_1="CaFluo"/>
      <map_variables variable_2="delta_CaFluo_rxn0" variable_1="delta_CaFluo_rxn0"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction2" component_1="CaFluo"/>
      <map_variables variable_2="CaFluo" variable_1="CaFluo"/>
      <map_variables variable_2="delta_CaFluo_rxn2" variable_1="delta_CaFluo_rxn2"/>
   </connection>
  
   <connection>
      <map_components component_2="reaction2" component_1="CaPrFluo"/>
      <map_variables variable_2="CaPrFluo" variable_1="CaPrFluo"/>
      <map_variables variable_2="delta_CaPrFluo_rxn2" variable_1="delta_CaPrFluo_rxn2"/>
   </connection>
   
   <connection>
      <map_components component_2="reaction3" component_1="CaPrFluo"/>
      <map_variables variable_2="CaPrFluo" variable_1="CaPrFluo"/>
      <map_variables variable_2="delta_CaPrFluo_rxn3" variable_1="delta_CaPrFluo_rxn3"/>
   </connection>
   
   <connection>
      <map_components component_2="environment" component_1="Ca"/>
      <map_variables variable_2="time" variable_1="time"/>
   </connection>
  
   <connection>
      <map_components component_2="environment" component_1="Fluo"/>
      <map_variables variable_2="time" variable_1="time"/>
   </connection>
  
   <connection>
      <map_components component_2="environment" component_1="Pr"/>
      <map_variables variable_2="time" variable_1="time"/>
   </connection>
  
   <connection>
      <map_components component_2="environment" component_1="PrFluo"/>
      <map_variables variable_2="time" variable_1="time"/>
   </connection>
  
   <connection>
      <map_components component_2="environment" component_1="CaFluo"/>
      <map_variables variable_2="time" variable_1="time"/>
   </connection>
  
   <connection>
      <map_components component_2="environment" component_1="CaPrFluo"/>
      <map_variables variable_2="time" variable_1="time"/>
   </connection>

<rdf:RDF>
  <rdf:Bag rdf:about="rdf:#10a76e66-f662-429e-a260-78cfd12c745b">
    <rdf:li>skeletal muscle</rdf:li>
    <rdf:li>calcium dynamics</rdf:li>
  </rdf:Bag>
  <rdf:Seq rdf:about="rdf:#208da49d-bc41-40f9-8c75-eac964adc525">
    <rdf:li rdf:resource="rdf:#ae55bd43-3625-417a-87c7-45df24e0be4a"/>
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