Location: Fallon, Lauffenburger, 2000 @ 5d88329ef5ce / fallon_lauffenburger_2000.cellml

Author:
pmr2.import <nobody@models.cellml.org>
Date:
2006-07-09 07:17:18+12:00
Desc:
committing version01 of fallon_lauffenburger_2000
Permanent Source URI:
https://staging.physiomeproject.org/workspace/fallon_lauffenburger_2000/rawfile/5d88329ef5ceeeaa85a5fc1132ecfb9f4d632bcc/fallon_lauffenburger_2000.cellml

<?xml version='1.0' encoding='utf-8'?>
<!--  FILE :fallon_model_2000.xml

CREATED :  16th 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 Fallon and Lauffenburger's 2000 model of the effects of ligand-receptor binding properties on interleukin-2 trafficking dynamics and T cell proliferation response.

CHANGES:  
  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="fallon_lauffenburger_2000_version01" name="fallon_lauffenburger_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
  <articleinfo>
  <title>Binding, Internalisation and Postendocytotic Sorting of Interleukin-2 and Its 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>
Interleukin-2 (IL-2) is a growth factor which is secreted by activated T-cells and which is responsible for stimulating T-cell proliferation.  Following the binding of the cell surface IL-2 receptor to its ligand, the entire receptor-ligand complex is internalised into sorting endosomes by endocytosis.  Within these endosomes, the receptor-ligand complex may dissociate, and also, internal receptors and ligands may associate to form a new complex.  Receptor associated ligand is then subject to lysosomal degradation, while free intracellular ligand is recycled back to extracellular ligand.  In the absence of any ligand, cell surface receptors are maintained at a steady level by constitutive internalisation and biosynthesis rates.  In the presence of ligand, there are positive feedback effects.  Cell surface receptor-ligand complexes stimulate the synthesis of new receptors, and they also enhance cell proliferation.     
</para>

<para>
Eric M. Fallon and Douglas A. Lauffenburger capture these IL-2 trafficking dynamics in their computational model (see <xref linkend="fig_reaction_diagram"/> below).  The model uses kinetic equations to describe receptor-ligand binding, internalisation and postendocytotic sorting of IL-2 and the IL-2-receptor complex.  Model simulations are able to predict T-cell proliferation responses to IL-2.  
</para>

<para>
The complete original paper reference is cited below:
</para>

<para>
<ulink url="http://pubs.acs.org/journals/bipret/abstract.cgi/bipret/2000/16/i05/abs/bp000097t.html">Computational Model for Effects of Ligand/Receptor Binding Properties on Interleukin-2 Trafficking Dynamics and T Cell Proliferation Response</ulink>, Eric M. Fallon and Douglas A. Lauffenburger, 2000, <ulink url="http://pubs.acs.org/journals/bipret/index.html">
            <emphasis>Biotechnology Progress</emphasis>
          </ulink>, 16, 905-916.  <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=11027188&amp;dopt=Abstract">PubMed ID: 11027188</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_reaction_diagram">
<mediaobject>
  <imageobject>
    <objectinfo>
      <title>diagram of the ligand-receptor binding model</title>
    </objectinfo>
    <imagedata fileref="reaction_diagram.gif"/>
  </imageobject>
</mediaobject>
<caption>A schematic diagram of Fallon and Lauffenburger's 2000 computational model of IL-2-receptor binding and trafficking.  The model follows the path of an extracellular ligand as it is bound to a cell surface receptor, internalised, degraded or recycled.</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="picomolar">
      <unit units="mole" prefix="pico"/>
      <unit units="litre" exponent="-1"/>
   </units>
   
   <units name="minute">
      <unit units="second" multiplier="60.0"/>
   </units>
   
   <units name="flux">
      <unit units="picomolar" exponent="1"/>
      <unit units="minute" exponent="-1"/>
   </units>
   
   <units name="first_order_rate_constant">
      <unit units="minute" exponent="-1"/>
   </units>
  
   <units name="second_order_rate_constant">
      <unit units="picomolar" exponent="-1"/>
      <unit units="minute" exponent="-1"/>
   </units>
   
   <units base_units="yes" name="cell"/>
   
   <units name="L_per_cell">
      <unit units="litre"/>
      <unit units="cell" exponent="-1"/>
   </units>
   
   <units name="per_L_per_cell">
      <unit units="L_per_cell" exponent="-1"/>
   </units>
   
   <units name="Cells_per_litre">
      <unit units="cell"/>
      <unit units="litre" 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="minute" public_interface="out" name="time"/>
   </component>
   
   <!--
    The following components describe all the reactants and products involved in
    reactions. 
  -->
  
   <component cmeta:id="Ligand_i" name="Ligand_i">
      <variable units="picomolar" public_interface="out" name="Ligand_i" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_i_rxn2"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_i_rxn6"/>
      <variable units="minute" public_interface="in" name="time"/>
      <variable units="per_L_per_cell" public_interface="out" name="NA" initial_value="1.0"/>
      <variable units="L_per_cell" public_interface="out" name="Ve" initial_value="1.0E-14"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
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            </apply>
            <apply>
               <plus/>
               <apply>
                  <divide/>
                  <ci>delta_Ligand_i_rxn2</ci>
                  <apply>
                     <times/>
                     <ci>Ve</ci>
                     <ci>NA</ci>
                  </apply>
               </apply>
               <ci>delta_Ligand_i_rxn6</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Ligand_d" name="Ligand_d">
      <variable units="picomolar" public_interface="out" name="Ligand_d" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_d_rxn3"/>
      <variable units="minute" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Ligand_d</ci>
            </apply>
            <ci>delta_Ligand_d_rxn3</ci>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Ligand_receptor_complex_i" name="Ligand_receptor_complex_i">
      <variable units="picomolar" public_interface="out" name="Ligand_receptor_complex_i" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_receptor_complex_i_rxn1"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_receptor_complex_i_rxn2"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_receptor_complex_i_rxn3"/>
      <variable units="minute" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Ligand_receptor_complex_i</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Ligand_receptor_complex_i_rxn1</ci>
               <ci>delta_Ligand_receptor_complex_i_rxn2</ci>
               <ci>delta_Ligand_receptor_complex_i_rxn3</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Ligand_receptor_complex_s" name="Ligand_receptor_complex_s">
      <variable units="picomolar" public_interface="out" name="Ligand_receptor_complex_s" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_receptor_complex_s_rxn0"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_receptor_complex_s_rxn1"/>
      <variable units="minute" public_interface="in" name="time"/>
      <variable units="Cells_per_litre" public_interface="out" name="Y" initial_value="2.5E8"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Ligand_receptor_complex_s</ci>
            </apply>
            <apply>
               <plus/>
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               <ci>delta_Ligand_receptor_complex_s_rxn1</ci>
            </apply>
         </apply>
         
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Y</ci>
            </apply>
            <apply>
               <times/>
               <apply>
                  <minus/>
                  <apply>
                     <divide/>
                     <apply>
                        <times/>
                        <cn cellml:units="dimensionless"> 600.0 </cn>
                        <ci>Ligand_receptor_complex_s</ci>
                     </apply>
                     <apply>
                        <plus/>
                        <cn cellml:units="dimensionless"> 250.0 </cn>
                        <ci>Ligand_receptor_complex_s</ci>
                     </apply>
                  </apply>
                  <cn cellml:units="dimensionless"> 200.0 </cn>
               </apply>
               <cn cellml:units="dimensionless"> 1000.0 </cn>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Receptor_i" name="Receptor_i">
      <variable units="picomolar" public_interface="out" name="Receptor_i" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_i_rxn2"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_i_rxn3"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_i_rxn7"/>
      <variable units="minute" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Receptor_i</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Receptor_i_rxn2</ci>
               <ci>delta_Receptor_i_rxn3</ci>
               <ci>delta_Receptor_i_rxn7</ci>
            </apply>
         </apply>
      </math>
   </component>
  
   <component cmeta:id="Receptor_s" name="Receptor_s">
      <variable units="picomolar" public_interface="out" name="Receptor_s" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_s_rxn4"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_s_rxn5"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_s_rxn0"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_s_rxn7"/>
      <variable units="minute" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Receptor_s</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Receptor_s_rxn4</ci>
               <ci>delta_Receptor_s_rxn5</ci>
               <ci>delta_Receptor_s_rxn0</ci>
               <ci>delta_Receptor_s_rxn7</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Ligand" name="Ligand">
      <variable units="picomolar" public_interface="out" name="Ligand" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_rxn6"/>
      <variable units="flux" public_interface="in" name="delta_Ligand_rxn0"/>
      <variable units="minute" public_interface="in" name="time"/>
      <variable units="per_L_per_cell" public_interface="in" name="NA"/>
      <variable units="L_per_cell" public_interface="in" name="Ve"/>
      <variable units="Cells_per_litre" public_interface="in" name="Y"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
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                  <ci>time</ci>
               </bvar>
               <ci>Ligand</ci>
            </apply>
            <apply>
               <divide/>
               <apply>
                  <times/>
                  <apply>
                     <plus/>
                     <apply>
                        <times/>
                        <ci>delta_Ligand_rxn6</ci>
                        <ci>Ve</ci>
                        <ci>NA</ci>
                     </apply>
                     <ci>delta_Ligand_rxn0</ci>
                  </apply>
                  <ci>Y</ci>
               </apply>
               <ci>NA</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <component cmeta:id="Receptor_precursors" name="Receptor_precursors">
      <variable units="picomolar" public_interface="out" name="Receptor_precursors" initial_value="1.0"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_precursors_rxn4"/>
      <variable units="flux" public_interface="in" name="delta_Receptor_precursors_rxn5"/>
      <variable units="minute" public_interface="in" name="time"/>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
         <apply>
            <eq/>
            <apply>
               <diff/>
               <bvar>
                  <ci>time</ci>
               </bvar>
               <ci>Receptor_precursors</ci>
            </apply>
            <apply>
               <plus/>
               <ci>delta_Receptor_precursors_rxn4</ci>
               <ci>delta_Receptor_precursors_rxn5</ci>
            </apply>
         </apply>
      </math>
   </component>
   
   <!--
    The following components describe the reactions of the model.
  -->
  
   <component name="reaction0">
      <variable units="picomolar" public_interface="in" name="Ligand"/>
      <variable units="picomolar" public_interface="in" name="Receptor_s"/>
      <variable units="picomolar" public_interface="in" name="Ligand_receptor_complex_s"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_rxn0"/>
      <variable units="flux" public_interface="out" name="delta_Receptor_s_rxn0"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_receptor_complex_s_rxn0"/>
      <variable units="second_order_rate_constant" name="k0" initial_value="0.0012432"/>
      <variable units="first_order_rate_constant" name="k0_" initial_value="0.0138"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="yes">
         <variable_ref variable="Ligand">
            <role stoichiometry="1" direction="forward" delta_variable="delta_Ligand_rxn0" role="reactant"/>
         </variable_ref>
         <variable_ref variable="Receptor_s">
            <role stoichiometry="1" direction="forward" delta_variable="delta_Receptor_s_rxn0" role="reactant"/>
         </variable_ref>
         <variable_ref variable="Ligand_receptor_complex_s">
            <role stoichiometry="1" direction="forward" delta_variable="delta_Ligand_receptor_complex_s_rxn0" role="product"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <plus/>
                        <apply>
                           <times/>
                           <ci>k0</ci>
                           <ci>Ligand</ci>
                           <ci>Receptor_s</ci>
                        </apply>
                        <apply>
                           <minus/>
                           <apply>
                              <times/>
                              <ci>k0_</ci>
                              <ci>Ligand_receptor_complex_s</ci>
                           </apply>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
   
   <component name="reaction1">
      <variable units="picomolar" public_interface="in" name="Ligand_receptor_complex_s"/>
      <variable units="picomolar" public_interface="in" name="Ligand_receptor_complex_i"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_receptor_complex_s_rxn1"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_receptor_complex_i_rxn1"/>
      <variable units="first_order_rate_constant" name="k1" initial_value="0.04"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="no">
         <variable_ref variable="Ligand_receptor_complex_s">
            <role stoichiometry="1" delta_variable="delta_Ligand_receptor_complex_s_rxn1" role="reactant"/>
         </variable_ref>
         <variable_ref variable="Ligand_receptor_complex_i">
            <role stoichiometry="1" delta_variable="delta_Ligand_receptor_complex_i_rxn1" role="product"/>
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                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <times/>
                        <ci>k1</ci>
                        <ci>Ligand_receptor_complex_s</ci>
                     </apply>
                  </apply>
               </math>
            </role>
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   <component name="reaction2">
      <variable units="picomolar" public_interface="in" name="Ligand_receptor_complex_i"/>
      <variable units="picomolar" public_interface="in" name="Ligand_i"/>
      <variable units="picomolar" public_interface="in" name="Receptor_i"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_receptor_complex_i_rxn2"/>
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      <variable units="flux" public_interface="out" name="delta_Receptor_i_rxn2"/>
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      <variable units="second_order_rate_constant" name="k2_" initial_value="1.104E-4"/>
      <variable units="flux" name="rate"/>
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         <variable_ref variable="Ligand_receptor_complex_i">
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         <variable_ref variable="Ligand_i">
            <role stoichiometry="1" direction="forward" delta_variable="delta_Ligand_i_rxn2" role="product"/>
         </variable_ref>
         <variable_ref variable="Receptor_i">
            <role stoichiometry="1" direction="forward" delta_variable="delta_Receptor_i_rxn2" role="product"/>
         </variable_ref>
         <variable_ref variable="rate">
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               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <plus/>
                        <apply>
                           <times/>
                           <ci>k2</ci>
                           <ci>Ligand_receptor_complex_i</ci>
                        </apply>
                        <apply>
                           <minus/>
                           <apply>
                              <times/>
                              <ci>k2_</ci>
                              <ci>Ligand_i</ci>
                              <ci>Receptor_i</ci>
                           </apply>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
  
   <component name="reaction3">
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      <variable units="picomolar" public_interface="in" name="Receptor_i"/>
      <variable units="picomolar" public_interface="in" name="Ligand_d"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_receptor_complex_i_rxn3"/>
      <variable units="flux" public_interface="out" name="delta_Ligand_d_rxn3"/>
      <variable units="flux" public_interface="out" name="delta_Receptor_i_rxn3"/>
      <variable units="first_order_rate_constant" name="k3" initial_value="0.035"/>
      <variable units="flux" name="rate"/>
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         <variable_ref variable="Ligand_receptor_complex_i">
            <role stoichiometry="1" delta_variable="delta_Ligand_receptor_complex_i_rxn3" role="reactant"/>
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         <variable_ref variable="Ligand_d">
            <role stoichiometry="1" delta_variable="delta_Ligand_d_rxn3" role="product"/>
         </variable_ref>
         <variable_ref variable="Receptor_i">
            <role stoichiometry="1" delta_variable="delta_Receptor_i_rxn3" role="product"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <times/>
                        <ci>k3</ci>
                        <ci>Ligand_receptor_complex_i</ci>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
   
   <component name="reaction4">
      <variable units="picomolar" public_interface="in" name="Receptor_precursors"/>
      <variable units="picomolar" public_interface="in" name="Receptor_s"/>
      <variable units="flux" public_interface="out" name="delta_Receptor_precursors_rxn4"/>
      <variable units="flux" public_interface="out" name="delta_Receptor_s_rxn4"/>
      <variable units="first_order_rate_constant" name="k4" initial_value="0.0011"/>
      <variable units="flux" name="rate"/>
      <reaction reversible="no">
         <variable_ref variable="Receptor_precursors">
            <role stoichiometry="1" delta_variable="delta_Receptor_precursors_rxn4" role="reactant"/>
         </variable_ref>
         <variable_ref variable="Receptor_s">
            <role stoichiometry="1" delta_variable="delta_Receptor_s_rxn4" role="product"/>
         </variable_ref>
         <variable_ref variable="rate">
            <role role="rate">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <eq/>
                     <ci>rate</ci>
                     <apply>
                        <times/>
                        <ci>k4</ci>
                        <ci>Receptor_precursors</ci>
                     </apply>
                  </apply>
               </math>
            </role>
         </variable_ref>
      </reaction>
   </component>
  
   <component name="reaction5">
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      <variable units="picomolar" public_interface="in" name="Receptor_s"/>
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   <component name="reaction7">
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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   <connection>
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            Computational Model for Effects of Ligand/Receptor Binding 
            Properties on Interleukin-2 Trafficking Dynamics and T Cell 
            Proliferation Response
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          This is the CellML description of Fallon and Lauffenburger's 2000 
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    <dc:title>Biotechnology Progress</dc:title>
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        Fallon and Lauffenburger's 2000 model of the effects of ligand-receptor 
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