- 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_f.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE :baylor_model_f_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_f_2002" cmeta:id="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 is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
<para>
This model describes Two-step reaction between Ca2+ and troponin
</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&db=PubMed&list_uids=12198091&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_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>Ca</ci>
</apply>
<apply>
<plus/>
<ci>delta_Ca_rxn0</ci>
<ci>delta_Ca_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Trop" name="Trop">
<variable units="micromolar" public_interface="out" name="Trop" initial_value="360.0"/>
<variable units="flux" public_interface="in" name="delta_Trop_rxn0"/>
<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>Trop</ci>
</apply>
<ci>delta_Trop_rxn0</ci>
</apply>
</math>
</component>
<component cmeta:id="CaTrop" name="CaTrop">
<variable units="micromolar" public_interface="out" name="CaTrop"/>
<variable units="flux" public_interface="in" name="delta_CaTrop_rxn0"/>
<variable units="flux" public_interface="in" name="delta_CaTrop_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>CaTrop</ci>
</apply>
<apply>
<plus/>
<ci>delta_CaTrop_rxn0</ci>
<ci>delta_CaTrop_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Ca2Trop" name="Ca2Trop">
<variable units="micromolar" public_interface="out" name="Ca2Trop"/>
<variable units="flux" public_interface="in" name="delta_Ca2Trop_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>Ca2Trop</ci>
</apply>
<ci>delta_Ca2Trop_rxn1</ci>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="reaction0">
<variable units="micromolar" public_interface="in" name="Trop"/>
<variable units="micromolar" public_interface="in" name="Ca"/>
<variable units="micromolar" public_interface="in" name="CaTrop"/>
<variable units="flux" public_interface="out" name="delta_Trop_rxn0"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn0"/>
<variable units="flux" public_interface="out" name="delta_CaTrop_rxn0"/>
<variable units="second_order_rate_constant" name="k0" initial_value="2.033E8"/>
<variable units="first_order_rate_constant" name="k0_" initial_value="2642.0"/>
<variable units="flux" name="rate"/>
<reaction reversible="yes">
<variable_ref variable="Trop">
<role role="reactant" direction="forward" delta_variable="delta_Trop_rxn0" stoichiometry="1"/>
</variable_ref>
<variable_ref variable="Ca">
<role role="reactant" direction="forward" delta_variable="delta_Ca_rxn0" stoichiometry="1"/>
</variable_ref>
<variable_ref variable="CaTrop">
<role role="product" direction="forward" delta_variable="delta_CaTrop_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>Trop</ci>
<ci>Ca</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k0_</ci>
<ci>CaTrop</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction1">
<variable units="micromolar" public_interface="in" name="Ca"/>
<variable units="micromolar" public_interface="in" name="CaTrop"/>
<variable units="micromolar" public_interface="in" name="Ca2Trop"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn1"/>
<variable units="flux" public_interface="out" name="delta_CaTrop_rxn1"/>
<variable units="flux" public_interface="out" name="delta_Ca2Trop_rxn1"/>
<variable units="second_order_rate_constant" name="k1" initial_value="1.017E8"/>
<variable units="first_order_rate_constant" name="k1_" initial_value="13.21"/>
<variable units="flux" name="rate"/>
<reaction reversible="yes">
<variable_ref variable="Ca">
<role role="reactant" direction="forward" delta_variable="delta_Ca_rxn1" stoichiometry="1"/>
</variable_ref>
<variable_ref variable="CaTrop">
<role role="reactant" direction="forward" delta_variable="delta_CaTrop_rxn1" stoichiometry="1"/>
</variable_ref>
<variable_ref variable="Ca2Trop">
<role role="product" direction="forward" delta_variable="delta_Ca2Trop_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>Ca</ci>
<ci>CaTrop</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k1_</ci>
<ci>Ca2Trop</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="reaction1" component_1="Ca"/>
<map_variables variable_2="Ca" variable_1="Ca"/>
<map_variables variable_2="delta_Ca_rxn1" variable_1="delta_Ca_rxn1"/>
</connection>
<connection>
<map_components component_2="reaction0" component_1="Trop"/>
<map_variables variable_2="Trop" variable_1="Trop"/>
<map_variables variable_2="delta_Trop_rxn0" variable_1="delta_Trop_rxn0"/>
</connection>
<connection>
<map_components component_2="reaction0" component_1="CaTrop"/>
<map_variables variable_2="CaTrop" variable_1="CaTrop"/>
<map_variables variable_2="delta_CaTrop_rxn0" variable_1="delta_CaTrop_rxn0"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="CaTrop"/>
<map_variables variable_2="CaTrop" variable_1="CaTrop"/>
<map_variables variable_2="delta_CaTrop_rxn1" variable_1="delta_CaTrop_rxn1"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="Ca2Trop"/>
<map_variables variable_2="Ca2Trop" variable_1="Ca2Trop"/>
<map_variables variable_2="delta_Ca2Trop_rxn1" variable_1="delta_Ca2Trop_rxn1"/>
</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="Trop"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CaTrop"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Ca2Trop"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<rdf:RDF>
<rdf:Bag rdf:about="rdf:#84363bae-5d08-4fc0-8218-902a427c97c0">
<rdf:li>skeletal muscle</rdf:li>
<rdf:li>calcium dynamics</rdf:li>
</rdf:Bag>
<rdf:Seq rdf:about="rdf:#30446853-be7c-4e84-a423-088b0c58cb23">
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<rdf:li rdf:resource="rdf:#58785cad-847f-4e7f-974d-5b733d8b217e"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#57ec4e04-5150-4104-9c98-4fcb8ba7f0a6">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#fe614d3a-5eba-4587-8194-76960ad3120a">
<vCard:Given>S</vCard:Given>
<vCard:Family>Hollingworth</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="">
<dc:publisher>The University of Auckland, Bioengineering Institute</dc:publisher>
<cmeta:comment rdf:resource="rdf:#9155e7da-75ef-4387-a643-5e5ee07aa6d6"/>
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<vCard:Given>Autumn</vCard:Given>
<vCard:Family>Cuellar</vCard:Family>
<vCard:Other>A</vCard:Other>
</rdf:Description>
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<dcterms:W3CDTF>2002-11-01</dcterms:W3CDTF>
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<rdf:value>This is the CellML description of Baylor, Hollingworth and Chandler's 2002 model of the Two-step reaction between Ca2+ and troponin in skeletal myocytes.</rdf:value>
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<dc:title>Comparison of Simulated and Measured Calcium Sparks in Intact
Skeletal Muscle Fibers of the Frog</dc:title>
<bqs:volume>120</bqs:volume>
<bqs:first_page>349</bqs:first_page>
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<vCard:Given>S</vCard:Given>
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<dcterms:W3CDTF>2002-09-01</dcterms:W3CDTF>
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<dc:title>Journal of General Physiology</dc:title>
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<rdf:Description rdf:about="#baylor_model_f_2002">
<dc:title>
Baylor, Hollingworth and Chandler's 2002 model of the Ca2+-ATP binding
reaction in skeletal myocytes.
</dc:title>
<cmeta:bio_entity>Skeletal Myocyte</cmeta:bio_entity>
<cmeta:comment rdf:resource="rdf:#7e9f30a1-5be4-4cd8-960c-7c30b179caaa"/>
<bqs:reference rdf:resource="rdf:#420829e5-b057-413e-8ad3-3d335b406035"/>
<bqs:reference rdf:resource="rdf:#a95647e1-9ae1-4eed-a25c-fdecc49cc2ac"/>
<cmeta:species>Frog</cmeta:species>
</rdf:Description>
<rdf:Description rdf:about="rdf:#9c752fa0-bcf6-4c9a-b4d9-5e5b8067f567">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
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<vCard:Given>W</vCard:Given>
<vCard:Family>Chandler</vCard:Family>
<vCard:Other>K</vCard:Other>
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<dcterms:W3CDTF>2003-04-09</dcterms:W3CDTF>
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<dcterms:modified rdf:resource="rdf:#a121c92a-9e4f-4333-af90-be2b4ce26d7b"/>
<rdf:value>
Added publication date information.
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