- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-26 14:35:03+13:00
- Desc:
- modifying rdf files
- Permanent Source URI:
- https://models.cellml.org/workspace/7f1/rawfile/4d6408caaf3e7b1b86d33d53d26105360ef95347/baylor_hollingworth_chandler_2002_f/model/baylor_hollingworth_chandler_2002_f.cellml
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<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Comparison of simulated and measured calcium sparks in intact skeletal muscle fibers of the frog</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>This CellML model runs in OpenCell and COR and the units are consistent. There are no simple figures of concentration against time in the publication to compare the CellML model simulation output against.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>ABSTRACT: Calcium sparks in frog intact skeletal muscle fibers were modeled as stereotypical events that arise from a constant efflux of Ca(2+) from a point source for a fixed period of time (e.g., 2.5 pA of Ca(2+) current for 4.6 ms; 18 degrees C). The model calculates the local changes in the concentrations of free Ca(2+) and of Ca(2+) bound to the major intrinsic myoplasmic Ca(2+) buffers (troponin, ATP, parvalbumin, and the SR Ca(2+) pump) and to the Ca(2+) indicator (fluo-3). A distinctive feature of the model is the inclusion of a binding reaction between fluo-3 and myoplasmic proteins, a process that strongly affects fluo-3's Ca(2+)-reaction kinetics, its apparent diffusion constant, and hence the morphology of sparks. DeltaF/F (the change in fluo-3's fluorescence divided by its resting fluorescence) was estimated from the calculated changes in fluo-3 convolved with the microscope point-spread function. To facilitate comparisons with measured sparks, noise and other sources of variability were included in a random repetitive fashion to generate a large number of simulated sparks that could be analyzed in the same way as the measured sparks. In the initial simulations, the binding of Ca(2+) to the two regulatory sites on troponin was assumed to follow identical and independent binding reactions. These simulations failed to accurately predict the falling phase of the measured sparks. A second set of simulations, which incorporated the idea of positive cooperativity in the binding of Ca(2+) to troponin, produced reasonable agreement with the measurements. Under the assumption that the single channel Ca(2+) current of a ryanodine receptor (RYR) is 0.5-2 pA, the results suggest that 1-5 active RYRs generate an average Ca(2+) spark in a frog intact muscle fiber.</para>
<para>The original paper reference is cited below:</para>
<para>
Comparison of simulated and measured calcium sparks in intact skeletal muscle fibers of the frog, S.M. Baylor, S. Hollingworth and W.K. Chandler, 2002,
<emphasis>Journal of General Physiology</emphasis>
, 120, 349-368.
<ulink url="http://www.ncbi.nlm.nih.gov/pubmed/12198091">PubMed ID: 12198091</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<imagedata fileref="baylor_2002.png" />
</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 exponent="-1.0" units="micromolar" />
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<units name="micromolar">
<unit prefix="micro" units="mole" />
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<units name="first_order_rate_constant">
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<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
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<dcterms:description>rate constant of calcium release from calcium-bound troponin</dcterms:description>
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<dcterms:description>concentration of di-calcium-bound troponin</dcterms:description>
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<dcterms:description>rate constant of calcium binding to troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#baylor_2002f" semsim:modelName="baylor_hollingworth_chandler_2002_f" bqmodel:isDescribedBy="12198091">
<semsim:unknown>Skeletal Myocyte</semsim:unknown>
<semsim:modelName>baylor_2002f</semsim:modelName>
<semsim:unknown>Baylor, Hollingworth and Chandler's 2002 model of the Ca2+-ATP binding
reaction in skeletal myocytes.</semsim:unknown>
<semsim:unknown>Frog</semsim:unknown>
</rdf:Description>
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<semsim:isComputationalComponentFor>
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<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
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<dcterms:description>rate constant of calcium binding to troponin</dcterms:description>
</rdf:Description>
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<dcterms:description>rate constant of calcium release from calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#CaTrop.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
<dcterms:description>concentration of troponin buffer</dcterms:description>
</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.CaTrop">
<semsim:isComputationalComponentFor>
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<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca.CaTrop">
<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca.Ca">
<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_9">
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</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#Ca.Ca2Trop">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of di-calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca2Trop.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Trop.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.Trop">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of troponin buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#reaction_constants.k2_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.Ca2Trop">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_10">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of di-calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca2Trop.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca2Trop.Ca">
<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#CaTrop.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Trop.Trop">
<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
<dcterms:description>concentration of troponin buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca.k2_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca2Trop.CaTrop">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_13">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca2Trop.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#CaTrop.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca2Trop.k2_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.k2_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Trop.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.CaTrop">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#Ca2Trop.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium release from troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaTrop.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate constant of calcium binding to troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#CaTrop.Trop">
<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
<dcterms:description>concentration of troponin buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca2Trop.Ca2Trop">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_11">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
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</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of di-calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k2">
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<dcterms:description>rate constant of calcium binding to calcium-bound troponin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="baylor_hollingworth_chandler_2002_f.cellml#CaTrop.CaTrop">
<bqbiol:isPropertyOf rdf:resource="baylor_hollingworth_chandler_2002_f.cellml#entity_2" />
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</rdf:Description>
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</rdf:Description>
</rdf:RDF>
</model>
