- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-26 14:35:03+13:00
- Desc:
- modifying rdf files
- Permanent Source URI:
- http://models.cellml.org/workspace/7f1/rawfile/4d6408caaf3e7b1b86d33d53d26105360ef95347/nagerl_novo_mody_vergara_2000/model/nagerl_novo_mody_vergara_2000.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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semsim:modelName="nagerl_novo_mody_vergara_2000"
bqmodel:isDescribedBy="11106608">
<semsim:hasCellMLdocumentation><documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Ca2+ Binding Kinetics of Calbindin-D28k</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>
Rapid changes in intracellular calcium concentration ([Ca
<superscript>2+</superscript>
]
<subscript>i</subscript>
) are characteristic of Ca
<superscript>2+</superscript>
signalling. Following a stimulus, Ca
<superscript>2+</superscript>
flows into the cytoplasm through channels in the cell membrane, and it's released from intracellular stores such as the endoplasmic reticulum. Normal [Ca
<superscript>2+</superscript>
] is resumed by the actions of Ca
<superscript>2+</superscript>
pumps, exchangers, binding proteins (CBPs) and other buffers. Calbindin-D
<subscript>28k</subscript>
is a CBP which is present at high cytosolic concentrations in neurons such as cerebellar Purkinje cells and hippocampal granule cells. Together with its high cytosolic concentration, the ability of calbindin-D
<subscript>28k</subscript>
to bind up to four Ca
<superscript>2+</superscript>
ions at any one time suggests that it plays an important role in Ca
<superscript>2+</superscript>
buffering.
</para>
<para>
Little is known about the Ca
<superscript>2+</superscript>
binding kinetics of calbindin-D
<subscript>28k</subscript>
, or of CBPs in general. In their 2000 paper, Nagerl
<emphasis>et al.</emphasis>
describe a new method to measure the binding kinetics of calbindin-D
<subscript>28k</subscript>
, which involves flash photolysis of DM-nitrophen (DM-n), a caged Ca
<superscript>2+</superscript>
compound. A mathematical model, which included the Ca
<superscript>2+</superscript>
binding reactions of all the species in the solution (see
<xref linkend="fig_reaction_diagram" />
below), was fitted to the experimental data in order to determine realistic kinetic parameters. The results of their experiments suggested that calbindin-D
<subscript>28k</subscript>
has two kinetically distinct types of Ca
<superscript>2+</superscript>
binding sites, one high- and one low-affinity. This heterogeneity was captured by their mathematical model.
</para>
<para>The complete original paper reference is cited below:</para>
<para>
<ulink url="http://www.biophysj.org/cgi/content/abstract/79/6/3009">
Binding Kinetics of Calbindin-D
<subscript>28k</subscript>
Determined by Flash Photolysis of Caged Ca
<superscript>2+</superscript>
</ulink>
, U. Valentin Nagerl, David Novo, Istvan Mody and Julio L. Vergara, 2000,
<ulink url="http://www.biophysj.org/">
<emphasis>Biophysical Journal</emphasis>
</ulink>
, 79, 3009-3018. (
<ulink url="http://www.biophysj.org/cgi/content/full/79/6/3009">Full text</ulink>
and
<ulink url="http://www.biophysj.org/cgi/reprint/79/6/3009.pdf">PDF versions</ulink>
of the article are available to subscribers on the Biophysical Journal website.)
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=11106608&amp;dopt=Abstract">PubMed ID: 11106608</ulink>
</para>
<para>
The raw CellML descriptions of the model can be downloaded in various formats as described in
<xref linkend="sec_download_this_model" />
.
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction_diagram</title>
</objectinfo>
<imagedata fileref="nagerl_2000.png" />
</imageobject>
</mediaobject>
<caption>
Schematic diagram of the mathematical model used to simulate the dynamic redistribution of Ca
<superscript>2+</superscript>
generated by flash photolysis of DM-n. CaDM1, CaDM2, CaD and CaB represent the concentration of Ca
<superscript>2+</superscript>
bound to DM-n, dye and buffer, respectively. Alpha models the fraction of Ca
<superscript>2+</superscript>
-bound DM-n1 that is photolysed by the UV laser flash.
</caption>
</informalfigure>
</sect1>
</article>
</documentation></semsim:hasCellMLdocumentation>
<semsim:unknown>Nagerl et al's 2000 study of the binding kinetics of calbindin-D28k.</semsim:unknown>
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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>concentration of total calcium</dcterms:description>
</rdf:Description>
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<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
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</rdf:Description>
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<dcterms:description>dissociation rate constant of OGB-5N indicator</dcterms:description>
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</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaDM2.DM2">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_3"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#Bi.Bi_T">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_4"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>total concentration of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#DM1.DM_T">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_3"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaD.Ca">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaDM1.CaDM1">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_3"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#DM2_T.DM2">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_3"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaDM1.DM1">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_3"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaBi.CaBi">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_4"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#constants.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaBi.koff_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>dissociation rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#D.CaD">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaDM1.Ca">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaD.CaD">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#D.D">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#CaDM1.t_pulse">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023"/>
<dcterms:description>point of flash pulse delivery</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#DM1.DM1">
<bqbiol:isPropertyOf rdf:resource="./nagerl_novo_mody_vergara_2000.cellml#entity_3"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#DM1.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./nagerl_novo_mody_vergara_2000.cellml#constants.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296"/>
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
</rdf:RDF>
