- 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_c.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE :baylor_model_c_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_c_2002" cmeta:id="baylor_model_c_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 Competitive reaction of Ca2+ and Mg2+ with parvalbumin
</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="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>
<ci>delta_Ca_rxn0</ci>
</apply>
</math>
</component>
<component cmeta:id="Parv" name="Parv">
<variable units="micromolar" public_interface="out" name="Parv" initial_value="1500.0"/>
<variable units="flux" public_interface="in" name="delta_Parv_rxn0"/>
<variable units="flux" public_interface="in" name="delta_Parv_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>Parv</ci>
</apply>
<apply>
<plus/>
<ci>delta_Parv_rxn0</ci>
<ci>delta_Parv_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="CaParv" name="CaParv">
<variable units="micromolar" public_interface="out" name="CaParv"/>
<variable units="flux" public_interface="in" name="delta_CaParv_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>CaParv</ci>
</apply>
<ci>delta_CaParv_rxn0</ci>
</apply>
</math>
</component>
<component cmeta:id="Mg" name="Mg">
<variable units="micromolar" public_interface="out" name="Mg" initial_value="1000.0"/>
<variable units="flux" public_interface="in" name="delta_Mg_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>Mg</ci>
</apply>
<ci>delta_Mg_rxn1</ci>
</apply>
</math>
</component>
<component cmeta:id="MgParv" name="MgParv">
<variable units="micromolar" public_interface="out" name="MgParv"/>
<variable units="flux" public_interface="in" name="delta_MgParv_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>MgParv</ci>
</apply>
<ci>delta_MgParv_rxn1</ci>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="reaction0">
<variable units="micromolar" public_interface="in" name="Parv"/>
<variable units="micromolar" public_interface="in" name="Ca"/>
<variable units="micromolar" public_interface="in" name="CaParv"/>
<variable units="flux" public_interface="out" name="delta_Parv_rxn0"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn0"/>
<variable units="flux" public_interface="out" name="delta_CaParv_rxn0"/>
<variable units="second_order_rate_constant" name="k0" initial_value="4.79E7"/>
<variable units="first_order_rate_constant" name="k0_" initial_value="0.574"/>
<variable units="flux" name="rate"/>
<reaction reversible="yes">
<variable_ref variable="Parv">
<role role="reactant" direction="forward" delta_variable="delta_Parv_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="CaParv">
<role role="product" direction="forward" delta_variable="delta_CaParv_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>Parv</ci>
<ci>Ca</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k0_</ci>
<ci>CaParv</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction1">
<variable units="micromolar" public_interface="in" name="Parv"/>
<variable units="micromolar" public_interface="in" name="Mg"/>
<variable units="micromolar" public_interface="in" name="MgParv"/>
<variable units="flux" public_interface="out" name="delta_Parv_rxn1"/>
<variable units="flux" public_interface="out" name="delta_Mg_rxn1"/>
<variable units="flux" public_interface="out" name="delta_MgParv_rxn1"/>
<variable units="second_order_rate_constant" name="k1" initial_value="39700.0"/>
<variable units="first_order_rate_constant" name="k1_" initial_value="3.45"/>
<variable units="flux" name="rate"/>
<reaction reversible="yes">
<variable_ref variable="Parv">
<role role="reactant" direction="forward" delta_variable="delta_Parv_rxn1" stoichiometry="1"/>
</variable_ref>
<variable_ref variable="Mg">
<role role="reactant" direction="forward" delta_variable="delta_Mg_rxn1" stoichiometry="1"/>
</variable_ref>
<variable_ref variable="MgParv">
<role role="product" direction="forward" delta_variable="delta_MgParv_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>Parv</ci>
<ci>Mg</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k1_</ci>
<ci>MgParv</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="reaction0" component_1="Parv"/>
<map_variables variable_2="Parv" variable_1="Parv"/>
<map_variables variable_2="delta_Parv_rxn0" variable_1="delta_Parv_rxn0"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="Parv"/>
<map_variables variable_2="Parv" variable_1="Parv"/>
<map_variables variable_2="delta_Parv_rxn1" variable_1="delta_Parv_rxn1"/>
</connection>
<connection>
<map_components component_2="reaction0" component_1="CaParv"/>
<map_variables variable_2="CaParv" variable_1="CaParv"/>
<map_variables variable_2="delta_CaParv_rxn0" variable_1="delta_CaParv_rxn0"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="Mg"/>
<map_variables variable_2="Mg" variable_1="Mg"/>
<map_variables variable_2="delta_Mg_rxn1" variable_1="delta_Mg_rxn1"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="MgParv"/>
<map_variables variable_2="MgParv" variable_1="MgParv"/>
<map_variables variable_2="delta_MgParv_rxn1" variable_1="delta_MgParv_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="Parv"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CaParv"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Mg"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="MgParv"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<rdf:RDF>
<rdf:Bag rdf:about="rdf:#96be9735-878e-4970-90f0-298e531db6f8">
<rdf:li>skeletal muscle</rdf:li>
<rdf:li>calcium dynamics</rdf:li>
</rdf:Bag>
<rdf:Seq rdf:about="rdf:#8dd5da60-b787-4e49-8ead-b46478630634">
<rdf:li rdf:resource="rdf:#594d6813-6fd4-4c0c-9629-5417c88eea93"/>
<rdf:li rdf:resource="rdf:#1483ab8c-4113-46af-a748-c6512e0e6c90"/>
<rdf:li rdf:resource="rdf:#ab5d4dc0-ab8a-43e9-ae44-48457462da56"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#7db5c148-998e-463f-ba32-5dfbb92a2c83">
<vCard:ORG rdf:resource="rdf:#e9e690b4-8a9e-4992-bc70-7fcaef89e8e7"/>
<vCard:EMAIL rdf:resource="rdf:#f0cfbd61-1ece-4ea9-9b65-af4125d6fc16"/>
<vCard:N rdf:resource="rdf:#cf76d53c-b960-4011-b9ab-11c6c7d2b238"/>
</rdf:Description>
<rdf:Description rdf:about="">
<dc:publisher>The University of Auckland, Bioengineering Institute</dc:publisher>
<cmeta:comment rdf:resource="rdf:#04faa5f0-95bd-49a4-8be5-5b8466ec1f6c"/>
<dcterms:created rdf:resource="rdf:#83c2c6da-fedc-4347-ad90-6045698d26fa"/>
<dc:creator rdf:resource="rdf:#7db5c148-998e-463f-ba32-5dfbb92a2c83"/>
<cmeta:modification rdf:resource="rdf:#cfa04ba9-4458-4893-b351-ebcc18486e80"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#e05d1131-0bb1-4b4d-b252-5bd275accf81">
<dcterms:W3CDTF>2003-04-09</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#e9e690b4-8a9e-4992-bc70-7fcaef89e8e7">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
</rdf:Description>
<rdf:Description rdf:about="rdf:#fa95d39f-9d8b-4291-9893-4f2239a3a2ba">
<vCard:Given>Autumn</vCard:Given>
<vCard:Family>Cuellar</vCard:Family>
<vCard:Other>A</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#f0cfbd61-1ece-4ea9-9b65-af4125d6fc16">
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#cfa04ba9-4458-4893-b351-ebcc18486e80">
<dcterms:modified rdf:resource="rdf:#e05d1131-0bb1-4b4d-b252-5bd275accf81"/>
<rdf:value>
Added publication date information.
</rdf:value>
<cmeta:modifier rdf:resource="rdf:#454a6ae6-6a4d-40ee-b1d6-484f2da39b59"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#190bc4ec-26ae-45fd-b416-9cf7d228c2aa">
<vCard:Given>W</vCard:Given>
<vCard:Family>Chandler</vCard:Family>
<vCard:Other>K</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#454a6ae6-6a4d-40ee-b1d6-484f2da39b59">
<vCard:N rdf:resource="rdf:#fa95d39f-9d8b-4291-9893-4f2239a3a2ba"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#cf76d53c-b960-4011-b9ab-11c6c7d2b238">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
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<dc:creator rdf:resource="rdf:#8dd5da60-b787-4e49-8ead-b46478630634"/>
<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>
<bqs:Journal rdf:resource="rdf:#687af47c-e619-4508-9956-f9dbe69596f1"/>
<dcterms:issued rdf:resource="rdf:#c5477634-e566-475c-8b44-0d53e37e1dc8"/>
<bqs:last_page>368</bqs:last_page>
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<rdf:Description rdf:about="rdf:#922c03f4-7ef5-4d87-bc93-ba293e69f224">
<dc:creator rdf:resource="rdf:#3bd73410-7dd6-4880-b03c-c9505321b8ca"/>
<rdf:value>This is the CellML description of Baylor, Hollingworth and Chandler's 2002 model of the Competitive reaction of Ca2+ and Mg2+ with parvalbumin in skeletal myocytes.</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4db77fd1-7a2c-488c-bfe0-b0b164a9faef">
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<rdf:value/>
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<rdf:Description rdf:about="rdf:#687af47c-e619-4508-9956-f9dbe69596f1">
<dc:title>Journal of General Physiology</dc:title>
</rdf:Description>
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<vCard:FN/>
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<rdf:Description rdf:about="rdf:#7cf6a82a-4e3b-4326-b06c-f6fd5b897e3a">
<vCard:Given>S</vCard:Given>
<vCard:Family>Baylor</vCard:Family>
<vCard:Other>M</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c5477634-e566-475c-8b44-0d53e37e1dc8">
<dcterms:W3CDTF>2002-09-01</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#ad82ad7a-0397-4250-a447-14bcf0145036">
<vCard:Given>S</vCard:Given>
<vCard:Family>Hollingworth</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1483ab8c-4113-46af-a748-c6512e0e6c90">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#ad82ad7a-0397-4250-a447-14bcf0145036"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#3bd73410-7dd6-4880-b03c-c9505321b8ca">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#83c2c6da-fedc-4347-ad90-6045698d26fa">
<dcterms:W3CDTF>2002-11-01</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="#baylor_model_c_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:#922c03f4-7ef5-4d87-bc93-ba293e69f224"/>
<bqs:reference rdf:resource="rdf:#2d194626-9cc2-4400-b97e-0c7477643533"/>
<bqs:reference rdf:resource="rdf:#4db77fd1-7a2c-488c-bfe0-b0b164a9faef"/>
<cmeta:species>Frog</cmeta:species>
</rdf:Description>
<rdf:Description rdf:about="rdf:#60b63364-a986-4152-b819-989be8cebf10">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value rdf:resource="rdf:#96be9735-878e-4970-90f0-298e531db6f8"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#2d194626-9cc2-4400-b97e-0c7477643533">
<dc:subject rdf:resource="rdf:#60b63364-a986-4152-b819-989be8cebf10"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#594d6813-6fd4-4c0c-9629-5417c88eea93">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#7cf6a82a-4e3b-4326-b06c-f6fd5b897e3a"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#ab5d4dc0-ab8a-43e9-ae44-48457462da56">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#190bc4ec-26ae-45fd-b416-9cf7d228c2aa"/>
</rdf:Description>
</rdf:RDF>
</model>
