- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2006-07-09 07:44:18+12:00
- Desc:
- committing version01 of lebeau_yule_groblewski_sneyd_1999
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/lebeau_yule_groblewski_sneyd_1999/rawfile/787b2020357027212e67f32f0c82904fbfb8a8ca/lebeau_yule_groblewski_sneyd_1999.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : lebeau_model_1999.xml
CREATED : 21st March 2002
LAST MODIFIED : 9th April 2003
AUTHOR : Catherine Lloyd
The Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/01/2002 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Andrew LeBeau et al's 1999 model for agonist-specific calcium oscillations in pancreatic acinar cells.
CHANGES:
18/07/2002 - CML - Added more metadata.
09/04/2003 - AAC - Added publication date information.
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="lebeau_yule_groblewski_sneyd_1999_version01" name="lebeau_yule_groblewski_sneyd_1999_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<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>
<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
</section>
<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>
<informalfigure float="0" id="fig_simplified_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A simplified diagram of the IPR model</title>
</objectinfo>
<imagedata fileref="lebeau_1999.png"/>
</imageobject>
</mediaobject>
<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>
</documentation>
<!--
Below, we define some additional units for association with variables and
constants within the model. The identifiers are fairly self-explanatory.
-->
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="flux">
<unit units="micromolar"/>
<unit units="second" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1"/>
</units>
<units name="second_order_rate_constant">
<unit units="micromolar" exponent="-1"/>
<unit units="second" exponent="-1"/>
</units>
<!--
The "environment" component is used to declare variables that are used by
all or most of the other components, in this case just "time".
-->
<component name="environment">
<variable units="second" public_interface="out" name="time"/>
</component>
<!--
The following components describe all the reactants and products involved in
reactions.
-->
<component cmeta:id="O" name="O">
<variable units="micromolar" public_interface="out" name="O"/>
<variable units="flux" public_interface="in" name="delta_O_rxn_1"/>
<variable units="flux" public_interface="in" name="delta_O_rxn_2"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>O</ci>
</apply>
<apply>
<plus/>
<ci>delta_O_rxn_1</ci>
<ci>delta_O_rxn_2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="I_1" name="I_1">
<variable units="micromolar" public_interface="out" name="I_1"/>
<variable units="flux" public_interface="in" name="delta_I_1_rxn_2"/>
<variable units="flux" public_interface="in" name="delta_I_1_rxn_3"/>
<variable units="flux" public_interface="in" name="delta_I_1_rxn_4"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>I_1</ci>
</apply>
<apply>
<plus/>
<ci>delta_I_1_rxn_2</ci>
<ci>delta_I_1_rxn_3</ci>
<ci>delta_I_1_rxn_4</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="I_2" name="I_2">
<variable units="micromolar" public_interface="out" name="I_2"/>
<variable units="flux" public_interface="in" name="delta_I_2_rxn_4"/>
<variable units="flux" public_interface="in" name="delta_I_2_rxn_5"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>I_2</ci>
</apply>
<apply>
<plus/>
<ci>delta_I_2_rxn_4</ci>
<ci>delta_I_2_rxn_5</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S" name="S">
<variable units="micromolar" public_interface="out" name="S"/>
<variable units="flux" public_interface="in" name="delta_S_rxn_1"/>
<variable units="flux" public_interface="in" name="delta_S_rxn_3"/>
<variable units="flux" public_interface="in" name="delta_S_rxn_5"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>S</ci>
</apply>
<apply>
<plus/>
<ci>delta_S_rxn_1</ci>
<ci>delta_S_rxn_3</ci>
<ci>delta_S_rxn_5</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="c" name="c">
<variable units="micromolar" public_interface="out" name="c"/>
<variable units="flux" name="J_rel"/>
<variable units="flux" name="J_pump"/>
<variable units="flux" name="J_influx" initial_value="0.4"/>
<variable units="flux" name="V_p" initial_value="2.6"/>
<variable units="micromolar" name="K_p" initial_value="0.54"/>
<variable units="flux" name="k_flux" initial_value="28.0"/>
<variable units="micromolar" public_interface="in" name="O"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>c</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>J_rel</ci>
<ci>J_pump</ci>
</apply>
<ci>J_influx</ci>
</apply>
</apply>
<apply id="J_rel_calculation">
<eq/>
<ci> J_rel </ci>
<apply>
<times/>
<ci> k_flux </ci>
<apply>
<power/>
<ci> O </ci>
<cn cellml:units="dimensionless"> 4.0 </cn>
</apply>
</apply>
</apply>
<apply id="J_pump_calculation">
<eq/>
<ci> J_pump </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> V_p </ci>
<apply>
<power/>
<ci> c </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> K_p </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
<apply>
<power/>
<ci> c </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="reaction1">
<variable units="micromolar" public_interface="in" name="S"/>
<variable units="micromolar" public_interface="in" name="O"/>
<variable units="flux" name="k_1a"/>
<variable units="first_order_rate_constant" name="k_1b" initial_value="0.88"/>
<variable units="flux" name="alpha_1" initial_value="40.0"/>
<variable units="micromolar" name="beta_1" initial_value="0.8"/>
<variable units="micromolar" public_interface="in" name="c"/>
<variable units="flux" public_interface="out" name="delta_S_rxn_1"/>
<variable units="flux" public_interface="out" name="delta_O_rxn_1"/>
<variable units="flux" name="r"/>
<reaction reversible="yes">
<variable_ref variable="S">
<role stoichiometry="1" direction="forward" delta_variable="delta_S_rxn_1" role="reactant"/>
</variable_ref>
<variable_ref variable="O">
<role stoichiometry="1" direction="forward" delta_variable="delta_O_rxn_1" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci> k_1a </ci>
<ci> S </ci>
</apply>
</apply>
<apply>
<times/>
<ci> O </ci>
<ci> k_1b </ci>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="k_1a_calculation">
<eq/>
<ci> k_1a </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> alpha_1 </ci>
<apply>
<power/>
<ci> c </ci>
<cn cellml:units="dimensionless"> 3.0 </cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> beta_1 </ci>
<cn cellml:units="dimensionless"> 3.0 </cn>
</apply>
<apply>
<power/>
<ci> c </ci>
<cn cellml:units="dimensionless"> 3.0 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="reaction2">
<variable units="micromolar" public_interface="in" name="I_1"/>
<variable units="micromolar" public_interface="in" name="O"/>
<variable units="first_order_rate_constant" name="k_2" initial_value="0.5"/>
<variable units="flux" public_interface="out" name="delta_O_rxn_2"/>
<variable units="flux" public_interface="out" name="delta_I_1_rxn_2"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="O">
<role stoichiometry="1" direction="forward" delta_variable="delta_O_rxn_2" role="reactant"/>
</variable_ref>
<variable_ref variable="I_1">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_1_rxn_2" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_2 </ci>
<ci> O </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction3">
<variable units="micromolar" public_interface="in" name="I_1"/>
<variable units="micromolar" public_interface="in" name="S"/>
<variable units="first_order_rate_constant" name="k_3" initial_value="0.5"/>
<variable units="flux" public_interface="out" name="delta_S_rxn_3"/>
<variable units="flux" public_interface="out" name="delta_I_1_rxn_3"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="I_1">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_1_rxn_3" role="reactant"/>
</variable_ref>
<variable_ref variable="S">
<role stoichiometry="1" direction="forward" delta_variable="delta_S_rxn_3" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_3 </ci>
<ci> I_1 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction4">
<variable units="micromolar" public_interface="in" name="I_1"/>
<variable units="micromolar" public_interface="in" name="I_2"/>
<variable units="first_order_rate_constant" name="k_4"/>
<variable units="first_order_rate_constant" name="alpha_4" initial_value="0.00"/>
<variable units="micromolar" name="beta_4" initial_value="0.01"/>
<variable units="micromolar" name="p"/>
<variable units="flux" public_interface="out" name="delta_I_2_rxn_4"/>
<variable units="flux" public_interface="out" name="delta_I_1_rxn_4"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="I_1">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_1_rxn_4" role="reactant"/>
</variable_ref>
<variable_ref variable="I_2">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_2_rxn_4" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w4.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_4 </ci>
<ci> I_1 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="k_4_calculation">
<eq/>
<ci> k_4 </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> alpha_4 </ci>
<ci> p </ci>
</apply>
<apply>
<plus/>
<ci> beta_4 </ci>
<ci> p </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="reaction5">
<variable units="micromolar" public_interface="in" name="I_2"/>
<variable units="micromolar" public_interface="in" name="S"/>
<variable units="first_order_rate_constant" name="k_5" initial_value="0.02"/>
<variable units="flux" public_interface="out" name="delta_S_rxn_5"/>
<variable units="flux" public_interface="out" name="delta_I_2_rxn_5"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="I_2">
<role stoichiometry="1" direction="forward" delta_variable="delta_I_2_rxn_5" role="reactant"/>
</variable_ref>
<variable_ref variable="S">
<role stoichiometry="1" direction="forward" delta_variable="delta_S_rxn_5" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_5 </ci>
<ci> I_2 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<connection>
<map_components component_2="environment" component_1="S"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="O"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="I_1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="I_2"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="c"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="S"/>
<map_variables variable_2="S" variable_1="S"/>
<map_variables variable_2="delta_S_rxn_1" variable_1="delta_S_rxn_1"/>
</connection>
<connection>
<map_components component_2="reaction3" component_1="S"/>
<map_variables variable_2="S" variable_1="S"/>
<map_variables variable_2="delta_S_rxn_3" variable_1="delta_S_rxn_3"/>
</connection>
<connection>
<map_components component_2="reaction5" component_1="S"/>
<map_variables variable_2="S" variable_1="S"/>
<map_variables variable_2="delta_S_rxn_5" variable_1="delta_S_rxn_5"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="O"/>
<map_variables variable_2="O" variable_1="O"/>
<map_variables variable_2="delta_O_rxn_1" variable_1="delta_O_rxn_1"/>
</connection>
<connection>
<map_components component_2="reaction2" component_1="O"/>
<map_variables variable_2="O" variable_1="O"/>
<map_variables variable_2="delta_O_rxn_2" variable_1="delta_O_rxn_2"/>
</connection>
<connection>
<map_components component_2="reaction2" component_1="I_1"/>
<map_variables variable_2="I_1" variable_1="I_1"/>
<map_variables variable_2="delta_I_1_rxn_2" variable_1="delta_I_1_rxn_2"/>
</connection>
<connection>
<map_components component_2="reaction3" component_1="I_1"/>
<map_variables variable_2="I_1" variable_1="I_1"/>
<map_variables variable_2="delta_I_1_rxn_3" variable_1="delta_I_1_rxn_3"/>
</connection>
<connection>
<map_components component_2="reaction4" component_1="I_1"/>
<map_variables variable_2="I_1" variable_1="I_1"/>
<map_variables variable_2="delta_I_1_rxn_4" variable_1="delta_I_1_rxn_4"/>
</connection>
<connection>
<map_components component_2="reaction4" component_1="I_2"/>
<map_variables variable_2="I_2" variable_1="I_2"/>
<map_variables variable_2="delta_I_2_rxn_4" variable_1="delta_I_2_rxn_4"/>
</connection>
<connection>
<map_components component_2="reaction5" component_1="I_2"/>
<map_variables variable_2="I_2" variable_1="I_2"/>
<map_variables variable_2="delta_I_2_rxn_5" variable_1="delta_I_2_rxn_5"/>
</connection>
<connection>
<map_components component_2="reaction1" component_1="c"/>
<map_variables variable_2="c" variable_1="c"/>
</connection>
<connection>
<map_components component_2="O" component_1="c"/>
<map_variables variable_2="O" variable_1="O"/>
</connection>
<rdf:RDF>
<rdf:Bag rdf:about="rdf:#46b275a8-e16c-4bbb-9a3e-e8257e4d051a">
<rdf:li>Pancreatic Acinar Cell</rdf:li>
<rdf:li>calcium dynamics</rdf:li>
</rdf:Bag>
<rdf:Seq rdf:about="rdf:#35cb6220-7508-4477-a54a-0f052739fd1f">
<rdf:li rdf:resource="rdf:#8e3d7078-ac72-4888-8384-23485d7ee34f"/>
<rdf:li rdf:resource="rdf:#3387a818-9577-46fb-bb30-a2ed6abd5ba5"/>
<rdf:li rdf:resource="rdf:#7517d21a-96a3-4078-bfd7-4f831a0de0b1"/>
<rdf:li rdf:resource="rdf:#1a5d8120-cb3b-4eb4-8c81-3865bc68a682"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#ff8cbf3d-5a53-4016-b3e8-79f1275908a8">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1a5d8120-cb3b-4eb4-8c81-3865bc68a682">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#d1b37447-adec-4be6-93d0-ff516f7ce595"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#da22acc5-31b9-4832-bcab-a98efa03bf5c">
<vCard:Given>David</vCard:Given>
<vCard:Family>Yule</vCard:Family>
<vCard:Other>I</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="#S">
<dcterms:alternative>Shut state</dcterms:alternative>
<dc:title>S</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#5512c7e4-2bb8-4518-8e9d-df5f07363af7">
<vCard:Given>Autumn</vCard:Given>
<vCard:Family>Cuellar</vCard:Family>
<vCard:Other>A</vCard:Other>
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Agonist-dependent Phosphorylation of the Inositol 1,4,5-Triphosphate Receptor
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