- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2009-06-17 16:20:24+12:00
- Desc:
- committing version03 of wanant_quon_2000
- Permanent Source URI:
- https://models.cellml.org/workspace/wanant_quon_2000/rawfile/752983f09025bbcae194debbd457418bc5bd6042/wanant_quon_2000_a.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : wanant_bimolecular_model_2000.xml
CREATED : 15th October 2002
LAST MODIFIED : 9th April 2003
AUTHOR : Catherine Lloyd
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 Wanant and Quon's
2000 divalent receptor model of insulin-receptor binding kinetics.
CHANGES:
09/04/2003 - AAC - Added publication date information.
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:NS3="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:NS2="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:NS5="http://www.cellml.org/metadata/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:NS7="http://www.cellml.org/metadata/simulation/1.0#" xmlns:NS1="http://www.cellml.org/bqs/1.0#" xmlns:RDF="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:NS4="http://purl.org/dc/elements/1.1/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:NS6="http://imc.org/vCard/3.0#" xmlns:ns7="http://www.cellml.org/metadata/simulation/1.0#" cmeta:id="wanant_quon_2000_version01" name="wanant_quon_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Insulin Receptor Binding Kinetics: A Divalent Receptor Model</title>
<author>
<firstname>James</firstname>
<surname>Lawson</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This version was created by James Lawson on 21/05/07 and is known to run in PCEnv. This file represents the divalent model described in Wanant and Quon 2000 'Insulin Receptor Binding Kinetics: Modeling and Simulation Studies.' Figures similar to those shown in the publication can be reproduced by graphing x1 (free insulin concentration, x axis) against 'scatchard,' which is a variable representing bound insulin over free insulin.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
The binding of the hormone insulin to its receptors embedded in the plasma membrane of hepatocytes and myocytes, is the initial step in a signal transduction pathway that mediates glucose uptake and metabolism. The mature insulin receptor is a transmembrane glycoprotein with a dimeric structure capable of binding two insulin molecules at any given moment. The kinetics of insulin receptor binding are complex. The affinity of the receptor for the second insulin molecule is significantly lower than for the first bound molecule. This may explain the negative cooperative interactions observed at high insulin concentrations. That is, as the concentration of insulin increases and more receptors become occupied, the affinity of the receptors for insulin decreases. Conversely, at low insulin concentrations, positive cooperativity has been recorded. That is, the binding of insulin to its receptor at low insulin concentrations seems to enhance further binding.
</para>
<para>
Sumanas Wanant and Michael J. Quon capture these features of insulin-receptor binding in their divalent receptor model (see <xref linkend="fig_receptor_diagram"/> below). A system of differential equations represented the receptor-ligand binding and dissociation reactions. The assigned parameter values were based on experimental data. Model simulations recreated the positive and negative cooperativity observed in experiments, providing supporting evidence for the accuracy of the model.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-45CWWW1-3V&_coverDate=08%2F07%2F2000&_alid=59985836&_rdoc=1&_fmt=summary&_orig=search&_qd=1&_cdi=6932&_sort=d&_acct=C000011498&_version=1&_urlVersion=0&_userid=140507&md5=7b4314936a107990fca425ea26020c08">Insulin Receptor Binding Kinetics: Modeling and Simulation Studies</ulink>, Sumanas Wanant and Michael J. Quon, 2000, <ulink url="http://www.sciencedirect.com/science?_ob=JournalURL&_cdi=6932&_auth=y&_acct=C000011498&_version=1&_urlVersion=0&_userid=140507&md5=c8e64d20ff203cda2255f4b6b7affe4f">
<emphasis>Journal of Theoretical Biology</emphasis>
</ulink>, 205, 355-364. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10882558&dopt=Abstract">PubMed ID: 10882558</ulink>
</para>
<para>
The raw CellML description of the model can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>
</para>
<informalfigure float="0" id="fig_receptor_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>diagram of the divalent receptor model</title>
</objectinfo>
<imagedata fileref="wanant_2000.png"/>
</imageobject>
</mediaobject>
<caption>A schematic diagram of Wanant and Quon's 2000 divalent insulin receptor model. This diagram shows a mature dimeric insulin receptor embedded in the plasma membrane. As it binds insulin molecules it changes from an unbound state, to a singly bound state, to a doubly bound state.</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="molar">
<unit units="mole"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="nanomolar">
<unit units="mole" prefix="nano"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="flux">
<unit units="molar" exponent="1"/>
<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="molar" 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="Insulin" name="Insulin">
<variable units="nanomolar" public_interface="out" name="x1" initial_value="1000"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<error xmlns="http://www.cellml.org/tools/mathml-input/error#" column="0" problem="syntax error"/>
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</bvar>
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<apply>
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<apply>
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<apply>
<minus/>
<apply>
<times/>
<ci>k1_</ci>
<ci>x3</ci>
</apply>
<apply>
<times/>
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<ci>x1</ci>
<ci>x2</ci>
</apply>
</apply>
<apply>
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<ci>k2_</ci>
<ci>x4</ci>
</apply>
</apply>
<apply>
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</apply>
</math>
<variable units="second_order_rate_constant" public_interface="in" name="k1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k1_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2_"/>
<variable units="nanomolar" public_interface="in" name="x2"/>
<variable units="nanomolar" public_interface="in" name="x3"/>
<variable units="nanomolar" public_interface="in" name="x4"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2"/>
<variable units="nanomolar" name="scatchard"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<apply>
<divide/>
<apply>
<plus/>
<ci>x3</ci>
<ci>x4</ci>
</apply>
<ci>x1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Unbound_receptor" name="Unbound_receptor">
<variable units="nanomolar" public_interface="out" name="x2" initial_value="0.1"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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</apply>
<apply>
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<ci>k1_</ci>
<ci>x3</ci>
</apply>
<apply>
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<ci>k1</ci>
<ci>x1</ci>
<ci>x2</ci>
</apply>
</apply>
</apply>
</math>
<variable units="nanomolar" public_interface="in" name="x1"/>
<variable units="nanomolar" public_interface="in" name="x3"/>
<variable units="second_order_rate_constant" public_interface="in" name="k1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k1_"/>
</component>
<component cmeta:id="single_bound_receptor" name="single_bound_receptor">
<variable units="nanomolar" public_interface="out" name="x3" initial_value=""/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci>x1</ci>
<ci>x2</ci>
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<apply>
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<ci>x3</ci>
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<apply>
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<ci>k2_</ci>
<ci>x4</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k2</ci>
<ci>x1</ci>
<ci>x3</ci>
</apply>
</apply>
</apply>
</math>
<variable units="nanomolar" public_interface="in" name="x1"/>
<variable units="nanomolar" public_interface="in" name="x2"/>
<variable units="nanomolar" public_interface="in" name="x4"/>
<variable units="second_order_rate_constant" public_interface="in" name="k1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k1_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2_"/>
</component>
<component cmeta:id="double_bound_receptor" name="double_bound_receptor">
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<error xmlns="http://www.cellml.org/tools/mathml-input/error#" column="0" problem="syntax error"/>
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<apply>
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<apply>
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</apply>
</apply>
</math>
<variable units="nanomolar" public_interface="out" name="x4" initial_value=""/>
<variable units="nanomolar" public_interface="in" name="x1"/>
<variable units="nanomolar" public_interface="in" name="x3"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2_"/>
</component>
<!--
The following components describe the reactions of the model.
-->
<connection>
<map_components component_2="environment" component_1="Insulin"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Unbound_receptor"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="single_bound_receptor"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="double_bound_receptor"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<component name="rate_constants">
<variable units="second_order_rate_constant" public_interface="out" name="k1" initial_value="1000000"/>
<variable units="first_order_rate_constant" public_interface="out" name="k1_" initial_value="0.0004"/>
<variable units="second_order_rate_constant" public_interface="out" name="k2" initial_value="1000000"/>
<variable units="first_order_rate_constant" public_interface="out" name="k2_" initial_value="0.04"/>
</component>
<connection>
<map_variables variable_2="k1" variable_1="k1"/>
<map_components component_2="Insulin" component_1="rate_constants"/>
<map_variables variable_2="k1_" variable_1="k1_"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k2_" variable_1="k2_"/>
</connection>
<connection>
<map_components component_2="Insulin" component_1="Unbound_receptor"/>
<map_variables variable_2="x2" variable_1="x2"/>
</connection>
<connection>
<map_components component_2="Insulin" component_1="single_bound_receptor"/>
<map_variables variable_2="x3" variable_1="x3"/>
</connection>
<connection>
<map_components component_2="Insulin" component_1="double_bound_receptor"/>
<map_variables variable_2="x4" variable_1="x4"/>
</connection>
<connection>
<map_components component_2="Unbound_receptor" component_1="rate_constants"/>
<map_variables variable_2="k1" variable_1="k1"/>
<map_variables variable_2="k1_" variable_1="k1_"/>
</connection>
<connection>
<map_components component_2="Unbound_receptor" component_1="Insulin"/>
<map_variables variable_2="x1" variable_1="x1"/>
</connection>
<connection>
<map_components component_2="Unbound_receptor" component_1="single_bound_receptor"/>
<map_variables variable_2="x3" variable_1="x3"/>
</connection>
<connection>
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<map_variables variable_2="k1" variable_1="k1"/>
<map_variables variable_2="k1_" variable_1="k1_"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k2_" variable_1="k2_"/>
</connection>
<connection>
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<map_variables variable_2="x1" variable_1="x1"/>
</connection>
<connection>
<map_components component_2="single_bound_receptor" component_1="Unbound_receptor"/>
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</connection>
<connection>
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</connection>
<connection>
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<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k2_" variable_1="k2_"/>
</connection>
<connection>
<map_components component_2="double_bound_receptor" component_1="Insulin"/>
<map_variables variable_2="x1" variable_1="x1"/>
</connection>
<connection>
<map_components component_2="double_bound_receptor" component_1="single_bound_receptor"/>
<map_variables variable_2="x3" variable_1="x3"/>
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<rdf:Description rdf:about="rdf:#4565f676-4ba9-4d94-b8c7-929bedf6ae26">
<dcterms:W3CDTF>2003-04-09</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#0fb13dbb-6386-4f14-9758-385b8ebebb35">
<dcterms:modified rdf:resource="rdf:#14fd55e8-b1f9-4516-a0e6-26281319e9b6"/>
<rdf:value>Fixed problem with units. Added a variable 'scatchard' in component 'insulin' which is defined by the equation: scatchard = (x3 + x4) / x1 and represents the 'bound/free' Scatchard axis.</rdf:value>
<cmeta:modifier rdf:resource="rdf:#31147dff-21a1-4f61-86b8-51204d3c8e17"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#440e7ba0-61d2-493b-9622-d0e76e00a82a">
<vCard:ORG rdf:resource="rdf:#a97dd2fb-4d07-4859-be50-7f2be4d93d60"/>
<vCard:EMAIL rdf:resource="rdf:#f1aad3d7-0d83-41c0-9da0-194424806277"/>
<vCard:N rdf:resource="rdf:#1668d973-5d1e-4c04-9f83-ea7fa1877865"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#2ae7a79e-1655-476b-8fd4-113b64546677">
<vCard:N rdf:resource="rdf:#024f77e4-f07d-4135-8e54-04354dba910b"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#dc09cb7d-751c-4d00-84fb-ba8ff037b37e">
<dc:creator rdf:resource="rdf:#39fe56e6-29bf-46cb-97a3-dbc04afda4aa"/>
<dc:title>Insulin receptor binding kinetics: modeling and simulation studies</dc:title>
<bqs:volume>205</bqs:volume>
<bqs:first_page>355</bqs:first_page>
<bqs:Journal rdf:resource="rdf:#85ff81b4-e56c-4a9e-8bda-f42c760faa41"/>
<dcterms:issued rdf:resource="rdf:#bcd7ede7-c1f6-45a5-8374-fe7d1e64c099"/>
<bqs:last_page>364</bqs:last_page>
</rdf:Description>
<rdf:Description rdf:about="#wanant_quon_2000_version01">
<ns7:simulation rdf:resource="rdf:#$oEFyV1"/>
<dc:title>Wanant and Quon's 2000 divalent receptor model of insulin-receptor
binding kinetics.</dc:title>
<cmeta:comment rdf:resource="rdf:#76a6c025-5598-4a1b-ac9f-53dda1efbb34"/>
<bqs:reference rdf:resource="rdf:#1a4b3046-a45f-4cb9-a180-1bb6644d3cda"/>
<bqs:reference rdf:resource="rdf:#c5b2f9a2-135d-4923-8509-5dbdcce6540d"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#ca50882d-18a5-4067-b05b-dd0d06aee358">
<vCard:Given>Michael</vCard:Given>
<vCard:Family>Quon</vCard:Family>
<vCard:Other>J</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#9e8f505c-a156-46d9-be97-0697071dc193">
<dc:creator rdf:resource="rdf:#94bbcc82-dc7b-4693-860b-1f8267caede0"/>
<rdf:value>This model has been rebuilt by James Lawson without using reaction elements, and is known to run in PCEnv, but does not currently produce the correct output. This variant corresponds to the divalent model.</rdf:value>
</rdf:Description>
</rdf:RDF>
</model>
