- 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/sneyd_dufour_2002/model/sneyd_dufour_2002.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:Description rdf:about="./sneyd_dufour_2002.cellml#open_probability.O">
<dcterms:description>fraction of IP3 receptors in open state</dcterms:description>
</rdf:Description>
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<rdf:Description rdf:about="./sneyd_dufour_2002.cellml#open_probability.open_probability">
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</rdf:Description>
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</bqbiol:isPropertyOf>
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</rdf:Description>
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</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>equilibrium constant</dcterms:description>
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</rdf:Description>
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</rdf:Description>
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<dcterms:description>fraction of IP3 receptors in inactivated I1state</dcterms:description>
</rdf:Description>
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<rdf:Description rdf:about="./sneyd_dufour_2002.cellml#sneyd_2002"
semsim:modelName="sneyd_2002"
bqmodel:isDescribedBy="11842185">
<semsim:unknown>The Sneyd-Dufour 2002 dynamic model of the type-2 inositol triphosphate receptor.@en</semsim:unknown>
<semsim:modelName>sneyd_dufour_2002</semsim:modelName>
<semsim:hasCellMLdocumentation><documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>A Dynamic Model Of The Type-2 Inositol Triphosphate Receptor</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 throughout. The model runs to recreate published results and is currently configured to recreate Figure 4 (Lower Plot, Trace 4), but variation of the IP3 and Calcium concentrations will allow the model to recreate different figures.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>ABSTRACT: The dynamic properties of the inositol (1,4,5)-trisphosphate (IP(3)) receptor are crucial for the control of intracellular Ca(2+), including the generation of Ca(2+) oscillations and waves. However, many models of this receptor do not agree with recent experimental data on the dynamic responses of the receptor. We construct a model of the IP(3) receptor and fit the model to dynamic and steady-state experimental data from type-2 IP(3) receptors. Our results indicate that, (i) Ca(2+) binds to the receptor using saturating, not mass-action, kinetics; (ii) Ca(2+) decreases the rate of IP(3) binding while simultaneously increasing the steady-state sensitivity of the receptor to IP(3); (iii) the rate of Ca(2+)-induced receptor activation increases with Ca(2+) and is faster than Ca(2+)-induced receptor inactivation; and (iv) IP(3) receptors are sequentially activated and inactivated by Ca(2+) even when IP(3) is bound. Our results emphasize that measurement of steady-state properties alone is insufficient to characterize the functional properties of the receptor.</para>
<para>The original paper reference is cited below:</para>
<para>
A dynamic model of the type-2 inositol triphosphate receptor, James Sneyd and Jean-Francois Dufour, 2002,
<emphasis>Proceedings of the National Academy of Sciences</emphasis>
, 99, 2398-2403.
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=11842185&amp;dopt=Abstract">PubMed ID: 11842185</ulink>
</para>
<informalfigure float="0" id="fig_simplified_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A simplified diagram of the IPR model</title>
</objectinfo>
<imagedata fileref="sneyd_2002.png" />
</imageobject>
</mediaobject>
<caption>A simplified diagram of the IPR model, where R represents the free receptor, O is the open state of the channel, A is the activated state of the channel and I1, I2, and S are three inactive states.</caption>
</informalfigure>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of intracellular calcium</dcterms:description>
</rdf:Description>
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</rdf:Description>
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<dcterms:description>fraction of IP3 receptors in open state</dcterms:description>
</rdf:Description>
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<dcterms:description>fraction of IP3 receptors in R state</dcterms:description>
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<dcterms:description>fraction of IP3 receptors in R state</dcterms:description>
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<dcterms:description>fraction of IP3 receptors in inactivated I2 state</dcterms:description>
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<dcterms:description>fraction of IP3 receptors in R state</dcterms:description>
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<dcterms:description>fraction of IP3 receptors in S state</dcterms:description>
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</rdf:Description>
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<dcterms:description>fraction of IP3 receptors in inactivated I2 state</dcterms:description>
</rdf:Description>
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</rdf:Description>
<rdf:Description rdf:about="./sneyd_dufour_2002.cellml#O_O">
<dcterms:description>fraction of IP3 receptors in open state</dcterms:description>
</rdf:Description>
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<dcterms:description>fraction of IP3 receptors in open state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./sneyd_dufour_2002.cellml#O.S">
<dcterms:description>fraction of IP3 receptors in S state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./sneyd_dufour_2002.cellml#O.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
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