- 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/dupont_1992a/model/dupont_1992a.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/">
<rdf:Description rdf:about="./dupont_1992a.cellml#cytosol.v0">
<dcterms:description>rate of influx of extracellular calcium into the cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#cytosol.kf">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>rate constant of passive leak of calcium from IP3-insensitive intracellular store into cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#cytosol.v2">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux from cytosol into the IP3-insensitive intracellular store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#Wstar">
<dcterms:description>fraction of phosphorylated protein</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.p">
<dcterms:description>Hill coefficient for calcium activation of IP3-insensitive store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.n">
<dcterms:description>Hill coefficient for calcium pumping into IP3-insensitive store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.VM2">
<dcterms:description>maximum rate of calcium pumping from cytosol into the IP3-insensitive intracellular store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#kinase_reaction.vMK">
<dcterms:description>effective maximal rate of kinase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#phosphorylation.K1">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>Michaelis-Menten constant of kinase</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
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</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#cytosol.v1beta">
<dcterms:description>rate of calcium release from the IP3-sensitive intracellular store into the cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#phosphorylation.WT">
<bqbiol:isPropertyOf>
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</rdf:Description>
</bqbiol:isPropertyOf>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>total concentration of protein substrate</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>reaction rate of kinase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#kinase_reaction.Z">
<bqbiol:isPropertyOf>
<rdf:Description rdf:about="./dupont_1992a.cellml#entity_0">
<bqbiol:isPartOf>
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<bqbiol:is rdf:resource="http://identifiers.org/go/GO:0005829"/>
</rdf:Description>
</bqbiol:isPartOf>
<bqbiol:is rdf:resource="https://identifiers.org/chebi/CHEBI:29108"/>
</rdf:Description>
</bqbiol:isPropertyOf>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.Z">
<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#cytosol.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#kinase_reaction.Ka">
<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>htreshold constant for activation of enzyme by cytosolic calcium</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_0"/>
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<dcterms:description>threshold constant for calcium activation of IP3-insensitive store</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#phosphorylation.Z">
<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of cytosolic calcium</dcterms:description>
</rdf:Description>
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>reaction rate of kinase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#environment_time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#insensitive_pool.v3">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux from IP3-insensitive intracellular store into the cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.k">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>rate constant of transport of cytosolic calcium out of the cell</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#cytosol.v3">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux from IP3-insensitive intracellular store into the cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#dupont_1992a"
bqmodel:isDescribedBy="1316185"
semsim:modelName="dupont_1992a">
<semsim:unknown>Protein phosphorylation driven by intracellular calcium oscillations: A kinetic analysis</semsim:unknown>
<semsim:hasCellMLdocumentation><documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Protein phosphorylation driven by intracellular calcium oscillations: A kinetic analysis</title>
<author>
<firstname>Ethan</firstname>
<surname>Choi</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>This model has been built with the differential expressions in Dupont and Goldbeter's 1992 paper. This file is known to run in PCEnv and COR, and variables for constants (K1 and K2) can be altered to produce all cases of figure 4 in the paper. The current parameterization is set to reproduce K1=K2 = 0.01 (note the erratum received in 1995: figure4c is produced by K1=K2=1, and not 10 as stated in the paper). Initial conditions for Z, Y and Wstar were set by letting the model settle into a steady state.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>Abstract: Given the ubiquitous nature of signal-induced Ca2+ oscillations, the question arises as to how cellular responses are affected by repetitive Ca2+ spikes. Among these responses, we focus on those involving protein phosphorylation. We examine, by numerical simulations of a theoretical model, the situation where a protein is phosphorylated by a Ca2+-activated kinase and dephosphorylated by a phosphatase. This reversible phosphorylation system is coupled to a mechanism generating cytosolic Ca2+ oscillations; for definiteness, this oscillatory mechanism is based on the process of Ca2+-induced Ca2+ release. The analysis shows that the average fraction of phosphorylated protein increases with the frequency of repetitive Ca2+ spikes; the latter frequency generally rises with the extent of external stimulation. Protein phosphorylation therefore provides a mechanism for the encoding of the external stimulation in terms of the frequency of signal-induced Ca2+ oscillations. Such a frequency encoding requires precise kinetic conditions on the Michaelis-Menten constants of the kinase and phosphatase, their maximal rates, and the degree of cooperativity in kinase activation by Ca2+. In particular, the most efficient encoding of Ca2+ oscillations based on protein phosphorylation occurs in conditions of zero-order ultrasensitivity, when the kinase and phosphatase are saturated by their protein substrate. The kinetic analysis uncovers a wide variety of temporal patterns of phosphorylation that could be driven by signal-induced Ca2+ oscillations.</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>model diagram</title>
</objectinfo>
<imagedata fileref="dupont_1992.png" />
</imageobject>
</mediaobject>
<caption>Schematic diagram of the cell model.</caption>
</informalfigure>
<para>The riginal paper reference is cited below:</para>
<para>
Protein phosphorylation driven by intracellular calcium oscillations: A kinetic analysis, Dupont G, Goldbeter A 1992,
<emphasis>Biophysical Chemistry</emphasis>
41, 257-270.
<ulink url="http://www.ncbi.nlm.nih.gov/pubmed/1316185">PubMedID: 1316185</ulink>
</para>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.KR">
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>threshold constant for calcium release from IP3-insensitive store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#metaid0">
<bqbiol:isPropertyOf>
<rdf:Description rdf:about="./dupont_1992a.cellml#entity_2">
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<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA:63842"/>
</rdf:Description>
</bqbiol:isPartOf>
<bqbiol:is rdf:resource="https://identifiers.org/chebi/CHEBI:29108"/>
</rdf:Description>
</bqbiol:isPropertyOf>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of calcium in IP3-insensitive intracellular store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.m">
<dcterms:description>Hill coefficient for calcium release from IP3-insensitive store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.KP">
<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>threshold constant for calcium pumping into IP3-insensitive store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.VM3">
<dcterms:description>maximum rate of calcium pumping from IP3-insensitive intracellular store into the cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.kf">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>rate constant of passive leak of calcium from IP3-insensitive intracellular store into cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#insensitive_pool.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.v2">
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>calcium flux from cytosol into the IP3-insensitive intracellular store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#kinase_reaction.q">
<dcterms:description>Hill coefficient for positive cooperativity of enzyme in the activation process</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#phosphorylation.K2">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>Michaelis-Menten constant of phosphatase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#phosphorylation.vP">
<dcterms:description>effective maximal rate of phosphatase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#parameters.Y">
<bqbiol:isPropertyOf rdf:resource="./dupont_1992a.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of calcium in IP3-insensitive intracellular store</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./dupont_1992a.cellml#Y">
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<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
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</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>rate constant of passive leak of calcium from IP3-insensitive intracellular store into cytosol</dcterms:description>
</rdf:Description>
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</rdf:Description>
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<dcterms:description>rate constant of transport of cytosolic calcium out of the cell</dcterms:description>
</rdf:Description>
</rdf:RDF>
