- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-25 19:32:58+13:00
- Desc:
- adding OMEX archives to workspace
- Permanent Source URI:
- http://models.cellml.org/workspace/7f1/rawfile/8a75fa307ab49aa87a6310ec8adf05ab8c95155f/cui_kaandorp_2006/model/cui_kaandorp_2006.rdf
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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="./cui_kaandorp_2006.cellml#x.h">
<dcterms:description>total nuclear fraction of Crz1p</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.V3">
<dcterms:description>rate parameter of Vcx1p</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#psi.L0">
<dcterms:description>basic equilibrium constant</dcterms:description>
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<dcterms:description>increment factor</dcterms:description>
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semsim:modelName="cui_kaandorp_2006"
bqmodel:isDescribedBy="16445978">
<semsim:unknown>Cui and Kaandorp's 2006 mathematical model of calcium homeostasis in yeast cells.</semsim:unknown>
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<article>
<articleinfo>
<title>Mathematical modelling of calcium homeostasis in yeast cells</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 model runs in OpenCell and COR. This version is able to reproduce figures from the original publication, although some tweeking of variables is required to produce the full range of figures. The model is currently parameterised to reproduce Fig 2a. The units have been checked and they are consistent.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>ABSTRACT: In this study, based on currently available experimental observations on protein level, we constructed a mathematical model to describe calcium homeostasis in normally growing yeast cells (Saccharomyces cerevisiae). Simulation results show that tightly controlled low cytosolic calcium ion level can be a natural result under the general mechanism of gene expression feedback control. The calmodulin (a sensor protein) behavior in our model cell agrees well with relevant observations in real cells. Moreover, our model can qualitatively reproduce the experimentally observed response curve of real yeast cell responding to step-like disturbance in extracellular calcium ion concentration. Further investigations show that the feedback control mechanism in our model is as robust as it is in real cells.</para>
<para>The original paper reference is cited below:</para>
<para>
Mathematical modeling of calcium homeostasis in yeast cells, Jiangjun Cui and Jaap A. Kaandorp, 2006,
<emphasis>Cell Calcium</emphasis>
, 39, 337-348.
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=16445978&amp;dopt=Abstract">PubMed ID: 16445978</ulink>
</para>
<informalfigure float="0" id="fig_simplified_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A schematic diagram of the model</title>
</objectinfo>
<imagedata fileref="cui_2006.png" />
</imageobject>
</mediaobject>
<caption>
A simplified diagram of the calcium fluxes described by the mathematical model. Extracellular calcium enters the cell cytosol through an unknown Channel X and also, under certain conditions such as depletion of secretory calcium, through the channel Cch1p-Mid1p. Cytosolic calcium can be pumped into the ER and Golgi through Pmrlp and into the vacuole through Pmc1p and Vcx1p. Under the abnormal condition of extracellular hypertonic shock, the vacuoles can release calcium into cytosol through Yvclp. Cytosolic calmodulin is a calcium-binding protein which in its bound form can activate target proteins such as calcineurin. Activated calcineurin dephosphorylates the transcription factor Crz1p, promoting its translocation into the nucleus where it regulates the transcription of genes such as
<emphasis>Pmr1</emphasis>
and
<emphasis>Pmc1</emphasis>
.
</caption>
</informalfigure>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
<semsim:modelName>cui_kaandorp_2006_version01</semsim:modelName>
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<dcterms:description>frequency of inactive conformation of Crz1p in the nucleus</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#phi.N">
<dcterms:description>number of relevant regulatory phosphorylation sites</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#phi.lamda">
<dcterms:description>increment factor</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#z.kN_minus">
<dcterms:description>backward rate constant of calcium binding to calcineurin reaction</dcterms:description>
</rdf:Description>
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<dcterms:description>basic equilibrium constant</dcterms:description>
</rdf:Description>
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<dcterms:description>total nuclear fraction of Crz1p</dcterms:description>
</rdf:Description>
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<dcterms:description>number of relevant regulatory phosphorylation sites</dcterms:description>
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</rdf:Description>
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<dcterms:description>nuclear import rate constant</dcterms:description>
</rdf:Description>
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</rdf:Description>
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<dcterms:description>rate of change of cytosolic calcium concentration</dcterms:description>
</rdf:Description>
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<dcterms:description>frequency of inactive conformation of Crz1p in the nucleus</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#psi.N">
<dcterms:description>number of relevant regulatory phosphorylation sites</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.kc">
<dcterms:description>feedback control constant</dcterms:description>
</rdf:Description>
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</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.V1">
<dcterms:description>rate parameter of Pmc1p</dcterms:description>
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</rdf:Description>
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<dcterms:description>cytosolic kinase level</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.K3">
<bqbiol:isPropertyOf rdf:resource="./cui_kaandorp_2006.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>binding constant of Vcx1p</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#h.phi">
<dcterms:description>frequency of active conformation of Crz1p in the cytosol</dcterms:description>
</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#m.kM_plus">
<dcterms:description>forward rate constant of calcium binding to calmodulin reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#phi.phi">
<dcterms:description>frequency of active conformation of Crz1p in the cytosol</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#m.kM_minus">
<dcterms:description>backward rate constant of calcium binding to calmodulin reaction</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="./cui_kaandorp_2006.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="./cui_kaandorp_2006.cellml#model_parameters.L0">
<dcterms:description>basic equilibrium constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#z.kN_plus">
<dcterms:description>forward rate constant of calcium binding to calcineurin reaction</dcterms:description>
</rdf:Description>
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<bqbiol:isPropertyOf rdf:resource="./cui_kaandorp_2006.cellml#entity_0"/>
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<dcterms:description>concentration of cytosolic calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#model_parameters.y">
<dcterms:description>cytosolic kinase level</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.V2">
<dcterms:description>rate parameter of Pmr1p</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.alpha">
<dcterms:description>growth rate constant of Crz1p</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#x.Vx">
<dcterms:description>rate parameter of channel X</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#h.f">
<dcterms:description>nuclear export rate constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#z.CaNtotal">
<bqbiol:isPropertyOf rdf:resource="./cui_kaandorp_2006.cellml#entity_0"/>
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<dcterms:description>total concentration of calcineurin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#model_parameters.lamda">
<dcterms:description>increment factor</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#psi.y">
<dcterms:description>cytosolic kinase level</dcterms:description>
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</rdf:Description>
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</rdf:Description>
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<dcterms:description>total concentration of calmodulin</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./cui_kaandorp_2006.cellml#z_z">
<bqbiol:isPropertyOf rdf:resource="./cui_kaandorp_2006.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of activated calcineurin</dcterms:description>
</rdf:Description>
</rdf:RDF>
