- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-24 22:38:46+13:00
- Desc:
- adding OMEX files to workspace
- Permanent Source URI:
- http://models.cellml.org/workspace/7f1/rawfile/c5103e98aa24310967dc95ab6549b142d317cfa8/lebeau_yule_groblewski_sneyd_1999/model/lebeau_yule_groblewski_sneyd_1999.cellml
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<article>
<articleinfo>
<title>Agonist-Dependent Phosphorylation Of The Inositol 1,4,5-Triphosphate Receptor</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>
The production of the intracellular signalling factor inositol 1,4,5-triphosphate (IP
<subscript>3</subscript>
) and the subsequent release of Ca
<superscript>2+</superscript>
stored in intracellular organelles is a fundamental cellular signalling function. The inositol triphosphate receptor (IPR) is an IP
<subscript>3</subscript>
-activated Ca
<superscript>2+</superscript>
channel in the ER. The properties of IP
<subscript>3</subscript>
-dependent intracellular calcium oscillations in pancreatic acinar cells depend on the agonist used to stimulate them.
</para>
<para>
This agonist-dependency is captured in Andrew P. LeBeau
<emphasis>et al's</emphasis>
1999 mathematical model of agonist-specific intracellular calcium oscillations in pancreatic acinar cells. They assume that the complete IPR is composed of four functionally identical, independent subunits, (see
<xref linkend="fig_simplified_diagram" />
below). IP
<subscript>3</subscript>
must be bound to all four subunits for the receptor to be in the conducting state.
</para>
<para>The complete original paper reference is cited below:</para>
<para>
<ulink url="http://www.jgp.org/cgi/content/abstract/113/6/851">Agonist-dependent Phosphorylation of the Inositol 1,4,5-Triphosphate Receptor. A Possible Mechanism for Agonist-specific Calcium Oscillations in Pancreatic Acinar Cells</ulink>
, Andrew P. LeBeau, David I. Yule, Guy E. Groblewski and James Sneyd, 1999,
<ulink url="http://www.jgp.org/">
<emphasis>The Journal Of General Physiology</emphasis>
</ulink>
, 113, 851-871. (
<ulink url="http://www.jgp.org/cgi/content/full/113/6/851">Full text</ulink>
and
<ulink url="http://www.jgp.org/cgi/reprint/113/6/851.pdf">PDF</ulink>
versions of the article are available to subscribers of the JGP website.)
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10352035&dopt=Abstract">PubMed ID: 10352035</ulink>
</para>
<para>
The raw CellML description of the dynamic model of the type-2 inositol triphosphate receptor can be downloaded in various formats as described in
<xref linkend="sec_download_this_model" />
.
</para>
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<title>A simplified diagram of the IPR model</title>
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<caption>
A diagram of the receptor states of the model of the IP
<subscript>3</subscript>
receptor. S denotes the fraction of the subunits in the shut state. Binding of IP
<subscript>3</subscript>
causes the receptor to be converted to the open state O. O is a relatively unstable state and the subunits will progress through to the more stable I
<subscript>1</subscript>
(inactivated) state in which IP
<subscript>3</subscript>
is still bound but the channels do not conduct. I
<subscript>2</subscript>
represents a second inactivated state of the receptor in which IP
<subscript>3</subscript>
is no longer bound.
</caption>
</informalfigure>
</sect1>
</article>
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<dcterms:description>fraction of IP3 receptor subunits in the I1 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.c">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_17">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of intracellular calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I2.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#I2.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#O.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.k4">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to I2 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.k5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I2 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.c">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>concentration of intracellular calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#c.J_influx">
<dcterms:description>calcium leak flux into cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#O.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#lebeau_model_1999_version02" bqmodel:isDescribedBy="10352035" />
<rdf:Description rdf:about="#I1.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to I1 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I1.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.beta_4">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>half-maximal activity IP3 constant of kinase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.k5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I2 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.k4">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to I2 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#I2.k5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I2 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#I2.I2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_7">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>fraction of IP3 receptor subunits in the I2 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.beta_1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_15">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_4">
<ro:part_of>
<rdf:Description rdf:about="#entity_5">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:63032" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/go/GO:0005829" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>half-maximal calcium constant of IP3 receptor shut to open transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.alpha_4">
<dcterms:description>maximum rate of kinase reaction at high IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#O.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to I1 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#O.p">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#c.O">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_13">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>fraction of IP3 receptor subunits in the open state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#c.K_p">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_12">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>half-maximal pumping constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#O.O">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>fraction of IP3 receptor subunits in the open state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#O.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to I1 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.k3">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#I2.I1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_8">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>fraction of IP3 receptor subunits in the I1 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#lebeau_model_1999_version02" bqmodel:isDescribedBy="10352035">
<semsim:modelName>lebeau_yule_groblewski_sneyd_1999_version01</semsim:modelName>
<semsim:modelName>lebeau_yule_groblewski_sneyd_1999</semsim:modelName>
<semsim:unknown>The LeBeau et al 1999 model for agaonist-specific calcium oscillations
in pancreatic acinar cells.</semsim:unknown>
<semsim:unknown>Pancreatic Acinar Cell</semsim:unknown>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#O.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of S to O transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.p">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_14">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#I2.k4">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to I2 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.alpha_4">
<dcterms:description>maximum rate of kinase reaction at high IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#O.I2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>fraction of IP3 receptor subunits in the I2 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#c.J_influx">
<dcterms:description>calcium leak flux into cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I1.k4">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to I2 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I1.I1">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>fraction of IP3 receptor subunits in the I1 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.k3">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to I1 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.k1_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I1.O">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>fraction of IP3 receptor subunits in the open state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#c.V_p">
<dcterms:description>maximum calcium pumping rate</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#O.S">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>fraction of IP3 receptor subunits in the shut state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#O.I1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>fraction of IP3 receptor subunits in the I1 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.p">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>concentration of IP3</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I1.k3">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#c.K_p">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>half-maximal pumping constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.beta_1">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>half-maximal calcium constant of IP3 receptor shut to open transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I2.k4">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I1 to I2 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I2.I1">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>fraction of IP3 receptor subunits in the I1 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#entity_1">
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA:63032" />
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.alpha_1">
<dcterms:description>maximum transition rate of IP3 receptor from shut to open state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of S to O transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.beta_4">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_16">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>half-maximal activity IP3 constant of kinase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#c.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I1.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to I1 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.alpha_1">
<dcterms:description>maximum transition rate of IP3 receptor from shut to open state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#constants.k1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of S to O transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#c.J_rel">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_10">
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>IP3-induced calcium flux out of the endoplasmic reticulum</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#c.c">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>concentration of intracellular calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I2.k5">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of I2 to S transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#O.k2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>rate of O to I1 transition</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#I2.I2">
<bqbiol:isPropertyOf rdf:resource="lebeau_yule_groblewski_sneyd_1999.cellml#entity_0" />
<dcterms:description>fraction of IP3 receptor subunits in the I2 state</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="lebeau_yule_groblewski_sneyd_1999.cellml#c.J_pump">
<dcterms:description>total calcium pumping flux out of the cytosol</dcterms:description>
</rdf:Description>
</rdf:RDF>
</model>
