- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2006-07-09 07:53:04+12:00
- Desc:
- committing version01 of stern_song_sham_yang_boheler_rios_1999
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/stern_song_sham_yang_boheler_rios_1999/rawfile/337908992b4518d0132842513511860435e3fa47/stern_song_sham_yang_boheler_rios_1999.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : stern_model_1999.xml
CREATED : 21st March 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 16/1/02 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Stern et al's
1999 model of ryanodine receptors in cardiac muscle.
CHANGES:
18/07/2002 - CML - Added more metadata.
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#" cmeta:id="stern_song_sham_yang_boheler_rios_1999_version01" name="stern_song_sham_yang_boheler_rios_1999_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Ryanodine Receptor Gating Kinetics in Cardiac Muscle</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>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
In cardiac muscle, release of activator calcium from the sarcoplasmic reticulum occurs by calcium-induced calcium release through ryanodine receptors (RyRs). In their 1999 paper, Michael D. Stern <emphasis>et al</emphasis> represented the ryanodine receptor with a phenomenological four-state gating scheme, with channel opening resulting from simultaneous binding of two Ca<superscript>2+</superscript> ions, and either calcium-dependent or activation-linked inactivation (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/113/3/469">Local Control Models of Cardiac Excitation-Contraction Coupling <emphasis>A Possible Role for Allosteric Interactions between Ryanodine Receptors</emphasis>
</ulink>, Michael D. Stern, Long-Sheng Song, Heping Cheng, James S.K. Sham, Huang Tian Yang, Kenneth R. Boheler and Eduardo Rios, 1999, <ulink url="http://www.jgp.org/">
<emphasis>The Journal Of General Physiology</emphasis>
</ulink>, 113, 469-489. (<ulink url="http://www.jgp.org/cgi/content/full/113/3/469">Full text</ulink> and <ulink url="http://www.jgp.org/cgi/reprint/113/3/469.pdf">PDF versions</ulink> of the article are available to subscribers on the JGP website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10051521&dopt=Abstract">PubMed ID: 10051521</ulink>
</para>
<para>
The raw CellML description of the kinetic model of cardiac ryanodine receptor gating 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>Schematic diagram of the RyR models</title>
</objectinfo>
<imagedata fileref="stern_1999.png"/>
</imageobject>
</mediaobject>
<caption>RyR gating scheme.</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="millimolar">
<unit units="mole" prefix="milli"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="millisecond">
<unit units="second" prefix="milli"/>
</units>
<units name="flux">
<unit units="millimolar"/>
<unit units="millisecond" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="millisecond" exponent="-1"/>
</units>
<units name="second_order_rate_constant">
<unit units="millimolar" exponent="-1"/>
<unit units="millisecond" exponent="-1"/>
</units>
<units name="third_order_rate_constant">
<unit units="millimolar" exponent="-2"/>
<unit units="millisecond" 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="millisecond" public_interface="out" name="time"/>
</component>
<!--
The following components describe all the reactants and products involved in
reactions.
-->
<component cmeta:id="R" name="R">
<variable units="millimolar" public_interface="out" name="R"/>
<variable units="flux" public_interface="in" name="delta_R_rxn_1"/>
<variable units="flux" public_interface="in" name="delta_R_rxn_4"/>
<variable units="millisecond" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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</bvar>
<ci>R</ci>
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<apply>
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<ci>delta_R_rxn_4</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="O" name="O">
<variable units="millimolar" public_interface="out" name="O"/>
<variable units="flux" public_interface="in" name="delta_O_rxn_1"/>
<variable units="flux" public_interface="in" name="delta_O_rxn_2"/>
<variable units="millisecond" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
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<bvar>
<ci>time</ci>
</bvar>
<ci>O</ci>
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<apply>
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<ci>delta_O_rxn_1</ci>
<ci>delta_O_rxn_2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="I" name="I">
<variable units="millimolar" public_interface="out" name="I"/>
<variable units="flux" public_interface="in" name="delta_I_rxn_2"/>
<variable units="flux" public_interface="in" name="delta_I_rxn_3"/>
<variable units="millisecond" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>I</ci>
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<ci>delta_I_rxn_3</ci>
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</math>
</component>
<component name="RI">
<variable units="millimolar" public_interface="out" name="RI"/>
<variable units="flux" public_interface="in" name="delta_RI_rxn_3"/>
<variable units="flux" public_interface="in" name="delta_RI_rxn_4"/>
<variable units="millisecond" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
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<bvar>
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</bvar>
<ci>RI</ci>
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<apply>
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<ci>delta_RI_rxn_4</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Ca" name="Ca">
<variable units="millimolar" public_interface="out" name="Ca"/>
<variable units="flux" public_interface="in" name="delta_Ca_rxn_1"/>
<variable units="flux" public_interface="in" name="delta_Ca_rxn_2"/>
<variable units="flux" public_interface="in" name="delta_Ca_rxn_3"/>
<variable units="flux" public_interface="in" name="delta_Ca_rxn_4"/>
<variable units="millisecond" 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_rxn_1</ci>
<ci>delta_Ca_rxn_2</ci>
<ci>delta_Ca_rxn_3</ci>
<ci>delta_Ca_rxn_4</ci>
</apply>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="reaction1">
<variable units="millimolar" public_interface="in" name="Ca"/>
<variable units="millimolar" public_interface="in" name="R"/>
<variable units="millimolar" public_interface="in" name="O"/>
<variable units="third_order_rate_constant" name="k_o" initial_value="35.0"/>
<variable units="first_order_rate_constant" name="k_om" initial_value="0.06"/>
<variable units="flux" public_interface="out" name="delta_R_rxn_1"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn_1"/>
<variable units="flux" public_interface="out" name="delta_O_rxn_1"/>
<variable units="flux" name="r"/>
<reaction reversible="yes">
<variable_ref variable="R">
<role stoichiometry="1" direction="forward" delta_variable="delta_R_rxn_1" role="reactant"/>
</variable_ref>
<variable_ref variable="Ca">
<role stoichiometry="2" direction="forward" delta_variable="delta_Ca_rxn_1" role="reactant"/>
</variable_ref>
<variable_ref variable="O">
<role stoichiometry="1" direction="forward" delta_variable="delta_O_rxn_1" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci> k_o </ci>
<ci> R </ci>
<apply>
<power/>
<ci> Ca </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> k_om </ci>
<ci> O </ci>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction2">
<variable units="millimolar" public_interface="in" name="Ca"/>
<variable units="millimolar" public_interface="in" name="O"/>
<variable units="millimolar" public_interface="in" name="I"/>
<variable units="second_order_rate_constant" name="k_i" initial_value="0.5"/>
<variable units="first_order_rate_constant" name="k_im" initial_value="0.005"/>
<variable units="flux" public_interface="out" name="delta_O_rxn_2"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn_2"/>
<variable units="flux" public_interface="out" name="delta_I_rxn_2"/>
<variable units="flux" name="r"/>
<reaction reversible="yes">
<variable_ref variable="O">
<role stoichiometry="1" direction="forward" delta_variable="delta_O_rxn_2" role="reactant"/>
</variable_ref>
<variable_ref variable="Ca">
<role stoichiometry="1" direction="forward" delta_variable="delta_Ca_rxn_2" role="reactant"/>
</variable_ref>
<variable_ref variable="I">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_rxn_2" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci> k_i </ci>
<ci> O </ci>
<ci> Ca </ci>
</apply>
</apply>
<apply>
<times/>
<ci> k_im </ci>
<ci> I </ci>
</apply>
</apply>
</apply>
</math>
</role>
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</component>
<component name="reaction3">
<variable units="millimolar" public_interface="in" name="Ca"/>
<variable units="millimolar" public_interface="in" name="I"/>
<variable units="millimolar" public_interface="in" name="RI"/>
<variable units="third_order_rate_constant" name="k_o" initial_value="35.0"/>
<variable units="first_order_rate_constant" name="k_om" initial_value="0.06"/>
<variable units="flux" public_interface="out" name="delta_I_rxn_3"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn_3"/>
<variable units="flux" public_interface="out" name="delta_RI_rxn_3"/>
<variable units="flux" name="r"/>
<reaction reversible="yes">
<variable_ref variable="I">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_rxn_3" role="reactant"/>
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<variable_ref variable="Ca">
<role stoichiometry="2" direction="forward" delta_variable="delta_Ca_rxn_3" role="reactant"/>
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<variable_ref variable="RI">
<role stoichiometry="1" direction="forward" delta_variable="delta_RI_rxn_3" role="product"/>
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<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<plus/>
<apply>
<minus/>
<apply>
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<ci> k_om </ci>
<ci> I </ci>
</apply>
</apply>
<apply>
<times/>
<ci> k_o </ci>
<ci> RI </ci>
<apply>
<power/>
<ci> Ca </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
</apply>
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<component name="reaction4">
<variable units="millimolar" public_interface="in" name="Ca"/>
<variable units="millimolar" public_interface="in" name="RI"/>
<variable units="millimolar" public_interface="in" name="R"/>
<variable units="second_order_rate_constant" name="k_i" initial_value="0.5"/>
<variable units="first_order_rate_constant" name="k_im" initial_value="0.005"/>
<variable units="flux" public_interface="out" name="delta_RI_rxn_4"/>
<variable units="flux" public_interface="out" name="delta_Ca_rxn_4"/>
<variable units="flux" public_interface="out" name="delta_R_rxn_4"/>
<variable units="flux" name="r"/>
<reaction reversible="yes">
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<role stoichiometry="1" direction="forward" delta_variable="delta_RI_rxn_4" role="reactant"/>
</variable_ref>
<variable_ref variable="Ca">
<role stoichiometry="1" direction="forward" delta_variable="delta_Ca_rxn_4" role="reactant"/>
</variable_ref>
<variable_ref variable="R">
<role stoichiometry="1" direction="forward" delta_variable="delta_R_rxn_4" role="product"/>
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<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<plus/>
<apply>
<minus/>
<apply>
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<ci> k_i </ci>
<ci> RI </ci>
<ci> Ca </ci>
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<apply>
<times/>
<ci> k_im </ci>
<ci> R </ci>
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</connection>
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<map_variables variable_2="delta_R_rxn_1" variable_1="delta_R_rxn_1"/>
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<connection>
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<connection>
<map_components component_2="reaction1" component_1="Ca"/>
<map_variables variable_2="Ca" variable_1="Ca"/>
<map_variables variable_2="delta_Ca_rxn_1" variable_1="delta_Ca_rxn_1"/>
</connection>
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<map_variables variable_2="Ca" variable_1="Ca"/>
<map_variables variable_2="delta_Ca_rxn_2" variable_1="delta_Ca_rxn_2"/>
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<map_components component_2="reaction3" component_1="Ca"/>
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</connection>
<rdf:RDF>
<rdf:Bag rdf:about="rdf:#4e183ec5-08bf-4501-a069-deacf50bb5ce">
<rdf:li>Cardiac Myocyte</rdf:li>
<rdf:li>calcium dynamics</rdf:li>
<rdf:li>ryanodine receptor</rdf:li>
</rdf:Bag>
<rdf:Seq rdf:about="rdf:#1d23b3a3-173a-42da-87f7-4a1b4627bccc">
<rdf:li rdf:resource="rdf:#a00e7a82-196f-41d7-a271-705c57d37131"/>
<rdf:li rdf:resource="rdf:#a7bb342d-3306-4930-8267-ff899a320c40"/>
<rdf:li rdf:resource="rdf:#da06e7ff-5975-4cb2-94f3-779f734b0ec1"/>
<rdf:li rdf:resource="rdf:#d563ae6c-9fbc-4fa6-8bb1-e932183b09b7"/>
<rdf:li rdf:resource="rdf:#eda39e9e-c858-4d8b-9f38-bbe8909f982e"/>
<rdf:li rdf:resource="rdf:#fce38d46-ff10-4746-8345-c9e5cbf0ed3e"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#6fc0e901-a963-45b1-91b1-f2bd34dfe393">
<dcterms:W3CDTF>2002-07-18</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#6c0cc0c0-ff00-4d72-a119-629e5c1e31ca">
<vCard:Given>Long-Sheng</vCard:Given>
<vCard:Family>Song</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#75bece84-264b-472e-b078-58006407345d">
<vCard:N rdf:resource="rdf:#4478d20d-a3c6-443a-b276-71182c5b420e"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4478d20d-a3c6-443a-b276-71182c5b420e">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#051adf88-68e8-45b6-b49c-e99757dfdcd0">
<vCard:Given>James</vCard:Given>
<vCard:Family>Sham</vCard:Family>
<vCard:Other>K</vCard:Other>
<vCard:Other>S</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#a7bb342d-3306-4930-8267-ff899a320c40">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#6c0cc0c0-ff00-4d72-a119-629e5c1e31ca"/>
</rdf:Description>
<rdf:Description rdf:about="#stern_song_sham_yang_boheler_rios_1999_version01">
<dc:title>
Stern et al's 1999 model of a gating scheme for ryanodine receptors.
</dc:title>
<cmeta:bio_entity>Cardiac Myocyte</cmeta:bio_entity>
<cmeta:comment rdf:resource="rdf:#36fe051d-9e21-4a1f-9137-51f1f046931d"/>
<bqs:reference rdf:resource="rdf:#22e08d68-7dbd-4bfb-8af0-2e3e6f8369e8"/>
<bqs:reference rdf:resource="rdf:#da651ad3-ca5a-4421-b996-7c4919016859"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#77417eed-7605-4fe9-9011-f387687071ab">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value rdf:resource="rdf:#4e183ec5-08bf-4501-a069-deacf50bb5ce"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c9931de3-18ce-4b9e-9b58-7285a4251968">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="#Ca">
<dcterms:alternative>Calcium concentration</dcterms:alternative>
<dc:title>Ca</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#3644d409-0b19-4728-9d3f-edadb5d81994">
<vCard:Given>Autumn</vCard:Given>
<vCard:Family>Cuellar</vCard:Family>
<vCard:Other>A</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="#I">
<dcterms:alternative>Inactive state</dcterms:alternative>
<dc:title>I</dc:title>
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Local Control Models of Cardiac Excitation-Contraction Coupling A Possible Role for Allosteric Interactions between Ryanodine Receptors
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