- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-25 18:50:11+13:00
- Desc:
- adding OMEX archives to workspace
- Permanent Source URI:
- http://models.cellml.org/workspace/7f1/rawfile/c5079f12eb1d8c164a111eea8277d5627c24a0b2/deyoung_keizer_1992/model/deyoung_keizer_1992.rdf
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:semsim="http://www.bhi.washington.edu/SemSim#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#mitochondrial_model_1992"
semsim:modelName="deyoung_keizer_1992"
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<semsim:unknown>IP3 Receptor</semsim:unknown>
<semsim:modelName>deyoung_keizer_1992_version01</semsim:modelName>
<semsim:unknown>The De Young-Keizer 1992 model of oscillatory calcium release through
the IP3 stimulated channel</semsim:unknown>
<semsim:hasCellMLdocumentation><documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>IP3-Mediated Ca2+ Release</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Ca
<superscript>2+</superscript>
is a ubiquitous intracellular secondary messenger, and evidence from several different cell types suggests that an important mode of signalling is through oscillations rather than the maintenance of a steady state level. The oscillatory behaviour of inositol 1,4,5-triphosphate (IP3)-mediated Ca
<superscript>2+</superscript>
release has been modelled by Gary W. De Young and Joel Keizer. Their 1992 paper is referenced fully below.
</para>
<para>
<ulink url="http://www.pnas.org/cgi/content/abstract/89/20/9895">
A single-pool inositol 1,4,5-triphosphate-receptor-based model for agonist-stimulated oscillations in Ca
<superscript>2+</superscript>
concentration
</ulink>
, Gary W. De Young and Joel Keizer, 1992,
<ulink url="http://www.pnas.org/">
<emphasis>Proc. Natl. Acad. Sci. USA</emphasis>
</ulink>
, 89, 9895-9899. (A
<ulink url="http://www.pnas.org/cgi/reprint/89/20/9895.pdf">PDF</ulink>
of the article is available to subscribers on the PNAS website.)
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=1329108&amp;dopt=Abstract">PubMed ID: 1329108</ulink>
</para>
<para>
Several mechanisms have been proposed to explain oscillations of intracellular Ca
<superscript>2+</superscript>
concentration in cells. In this study, De Young and Keizer investigate the idea that a biphasic response of the IP3 receptor/channel to cytosolic Ca
<superscript>2+</superscript>
may alone be sufficient to induce Ca
<superscript>2+</superscript>
oscillations.
</para>
<para>
They constructed a simplified model of the IP3 receptor/channel by assuming that three equivalent and independent subunits are involved in Ca
<superscript>2+</superscript>
conduction. Each subunit has three binding sites: one for IP3, one for Ca
<superscript>2+</superscript>
activation, and one for Ca
<superscript>2+</superscript>
inactivation. Thus each subunit may exist in eight states with transitions governed by second-order (association) and first-order (dissociation) rate constants (see
<xref linkend="fig_pathway_diagram" />
below). All three subunits must be in the state S
<subscript>110</subscript>
(one IP3 and one activating Ca
<superscript>2+</superscript>
bound) for the channel to be open and conducting.
</para>
<para>
The raw CellML description of the IP3-mediated Ca
<superscript>2+</superscript>
release model can be downloaded in various formats as described in
<xref linkend="sec_download_this_model" />
.
</para>
<informalfigure float="0" id="fig_pathway_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A schematic diagram of the kinetics of an IP3 receptor/channel subunit</title>
</objectinfo>
<imagedata fileref="deyoung_1992.png" />
</imageobject>
</mediaobject>
<caption>
A schematic diagram of the kinetics of an IP
<subscript>3</subscript>
receptor/channel subunit.
</caption>
</informalfigure>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
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<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_010.V3">
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</rdf:Description>
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</rdf:Description>
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</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#IP3.Ir">
<dcterms:description>rate constant for loss of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#IP3.IP3">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
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</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#IP3.alpha">
<dcterms:description>calcium stimulation factor of IP3 production</dcterms:description>
</rdf:Description>
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<dcterms:description>calcium inhibition receptor binding constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#receptor_dissociation_constants.a5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium activation receptor binding constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#fluxes.d4">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>calcium inhibition receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#Ca_ER.c0">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>total intracellular calcium in terms of cytosolic volume</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_001.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#constants.b2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium inhibition receptor binding constant multiplied by receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#receptor_dissociation_constants.b3">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>IP3 receptor binding constant multiplied by receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_001.V4">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>rate of conversion from IP3 receptor subunit state 001 to state 011</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#receptor_dissociation_constants.d3">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>IP3 receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_011.x_000">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of IP3 receptor subunit state 000 with free calcium activation site and free calcium inactivation site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#Ca_i.v3">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>maximum calcium uptake</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#fluxes.Ca_i">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#fluxes.V4">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>rate of conversion from IP3 receptor subunit state 001 to state 011</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#Ca_i.Ca_i">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#probability_of_an_open_IP3_receptor_channel.d5">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>calcium activation receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#probability_of_an_open_IP3_receptor_channel.d1">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>IP3 receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_000.V3">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>rate of conversion from IP3 receptor subunit state 000 to state 010</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#IP3.v4">
<dcterms:description>maximum rate of IP3 production</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#constants.a5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium activation receptor binding constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#Ca_i.c1">
<dcterms:description>ratio of endoplasmic reticulum volume to cytosolic volume</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#receptor_dissociation_constants.b4">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium inhibition receptor binding constant multiplied by receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#constants.d3">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>IP3 receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#receptor_dissociation_constants.d4">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>calcium inhibition receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#constants.a1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>IP3 receptor binding constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#constants.b3">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>IP3 receptor binding constant multiplied by receptor dissociation constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#fluxes.x_001">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of IP3 receptor subunit state 001 with free calcium activation site and occupied calcium inactivation site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#fluxes.a5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium activation receptor binding constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#receptor_dissociation_constants.a2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium inhibition receptor binding constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#probability_of_an_open_IP3_receptor_channel.IP3">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#Ca_ER.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#Ca_i.v2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>calcium leak flux constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_011.x_001">
<bqbiol:isPropertyOf rdf:resource="./deyoung_keizer_1992.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of IP3 receptor subunit state 001 with free calcium activation site and occupied calcium inactivation site</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./deyoung_keizer_1992.cellml#x_010.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
</rdf:RDF>
