Parent pages: SBML.org / Community / Wiki / SBML Level 3 Proposals / Multistate and Multicomponent Species Proposal

PhosphoReceptor

A receptor can bind a ligand, and be phosphorylated by a kinase. The phosphorylation can only take place on the free receptor. The binding reaction is stimulated by the phosphorylation.

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" 
             level="3" version="1"
             xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
             multi:required="true">

  <model>
    <listOfCompartments>
      <compartment id="cell" constant="true" size="1" />
    </listOfCompartments>

<!-- -------------------------------------------------------------------------------- -->
<!-- We need to define two species types to be able to describe all the reactions.    -->
<!-- There is not species type for the kinase, that is not used in selectors.         -->
<!-- -------------------------------------------------------------------------------- -->

    <multi:listOfSpeciesTypes>
      <multi:speciesType multi:id="st_recept"
                                          multi:name="receptor"
                                          multi:bindingSite="true">
        <multi:listOfStateFeatures>
          <multi:stateFeature multi:id="Y" multi:name="tyrosine">
            <multi:listOfPossibleValues>
               <multi:possibleValue multi:id="P" multi:name="phosphorylated" />
               <multi:possibleValue multi:id="nonP" multi:name="nonphosphorylated" />
            </multi:listOfPossibleValues>
          </multi:stateFeature>
        </multi:listOfStateFeatures>
      </multi:speciesType>

      <multi:speciesType multi:id="st_lig" multi:name="ligand" multi:bindingSite="true" />
    </multi:listOfSpeciesTypes>

    <multi:listOfSelectors>

<!-- -------------------------------------------------------------------------------- -->
<!-- Description of receptor, unbound, unphosphorylated                               -->
<!-- -------------------------------------------------------------------------------- -->
      <multi:selector multi:id="sel_freereceptor_nonP">

        <multi:listOfSpeciesTypeStates>
          <multi:speciesTypeState
                       multi:id="sts_recept" 
                       multi:speciesType="st_recept"
                       multi:minOccur="1" multi:maxOccur="1" >

            <multi:listOfStateFeatureInstances>
              <multi:stateFeatureInstance multi:stateFeature="Y">
                <multi:stateFeatureValue multi:possibleValue="nonphosphorylated" />
              </multi:stateFeatureInstance>
            </multi:listOfStateFeatureInstances>
          </multi:speciesTypeState>
        </multi:listOfSpeciesTypeStates>

        <multi:listOfUnboundBindingSites>
          <multi:bindingSiteReference multi:speciesTypeState="sts_recept" />
        </multi:listOfUnboundBindingSites>
      </multi:selector>

<!-- -------------------------------------------------------------------------------- -->
<!-- Description of receptor, unbound, phosphorylated                                 -->
<!-- -------------------------------------------------------------------------------- -->
      <multi:selector multi:id="sel_freereceptor_P">
        <multi:listOfSpeciesTypeStates>
          <multi:speciesTypeState 
                       multi:id="sts_recept" 
                       multi:speciesType="st_recept"
                       multi:minOccur="1" multi:maxOccur="1">
            <multi:listOfStateFeatureInstances>
              <multi:stateFeatureInstance multi:stateFeature="Y">
                <multi:stateFeatureValue multi:possibleValue="phosphorylated" />
              </multi:stateFeatureInstance>
            </multi:listOfStateFeatureInstances>
          </multi:speciesTypeState>
        </multi:listOfSpeciesTypeStates>

        <multi:listOfUnboundBindingSites>
          <multi:bindingSiteReference multi:speciesTypeState="sts_recept" />
        </multi:listOfUnboundBindingSites>
      </multi:selector>

<!-- -------------------------------------------------------------------------------- -->
<!-- Description of ligand, unbound                                                   -->
<!-- -------------------------------------------------------------------------------- -->
      <multi:selector multi:id="sel_freeligand">
        <multi:listOfSpeciesTypeStates>
          <multi:speciesTypeState 
                       multi:id="sts_lig" 
                       multi:speciesType="st_lig"
                       multi:minOccur="1" multi:maxOccur="1" />
        </multi:listOfSpeciesTypeStates>
          
        <multi:listOfUnboundBindingSites>
          <multi:bindingSiteReference multi:speciesTypeState="sts_lig" />
        </multi:listOfUnboundBindingSites>
      </multi:selector>

<!-- -------------------------------------------------------------------------------- -->
<!-- Description of the ligand-receptor complex                                       -->
<!-- -------------------------------------------------------------------------------- -->
      <multi:selector multi:id="sel_complex">
        <multi:listOfSpeciesTypeStates>
          <multi:speciesTypeState 
                       multi:id="sts_recept" 
                       multi:speciesType="st_recept"
                       multi:minOccur="1" multi:maxOccur="1" />

          <multi:speciesTypeState 
                       multi:id="sts_lig" 
                       multi:speciesType="st_lig"
                       multi:minOccur="1" multi:maxOccur="1" />
        </multi:listOfSpeciesTypeStates>

        <multi:listOfBonds>
          <multi:bond multi:occurrence="required">
            <multi:bindingSiteReference multi:speciesTypeState="sts_lig" />
            <multi:bindingSiteReference multi:speciesTypeState="sts_recept" />
          </multi:bond>
        </multi:listOfBonds>
      </multi:selector>
    </multi:listOfSelectors>

    <listOfSpecies>
      <species id="kinase" 
                       compartment="cell" boundaryCondition="false"
                       hasOnlySubstanceUnit="false" constant="false" 
                       initialAmount="100" />

      <species id="recept" 
                       multi:speciesType="st_recept"
                       compartment="cell" boundaryCondition="false" 
                       hasOnlySubstanceUnit="false" constant="false" 
                       initialAmount="100" >
        <multi:listOfSpeciesTypeInstances>
          <multi:SpeciesTypeInstance 
                       multi:id="freereceptor_nonP"
                       multi:initialAmount="100">
            <multi:listOfSelectorReferences>
              <multi:selectorReference multi:selector="sel_freereceptor_nonP" />
            </multi:listOfSelectorReferences>
          </multi:speciesTypeInstance>

          <multi:SpeciesTypeInstance 
                       multi:id="freereceptor_P"
                       multi:initialAmount="0">
            <multi:listOfSelectorReferences>
              <multi:selectorReference multi:selector="sel_freereceptor_P" />
            </multi:listOfSelectorReferences>
          </multi:speciesTypeInstance>

          <multi:SpeciesTypeInstance multi:id="boundreceptor">
            <multi:listOfSelectorReferences>
              <multi:selectorReference multi:selector="sel_complex">
            </multi:listOfSelectorReferences>
          </multi:speciesTypeInstance>
        </multi:listOfSpeciesTypeInstances>
      </species>

      <species id="lig" 
                       multi:speciesType="st_lig"
                       compartment="cell" boundaryCondition="false"
                       hasOnlySubstanceUnit="false" constant="false" 
                       initialAmount="1000" >
        <multi:listOfSpeciesTypeInstances>
          <multi:SpeciesTypeInstance multi:id="freeligand" multi:initialAmount="1000">
            <multi:listOfSelectorReferences>
              <multi:selectorReference multi:selector="sel_freeligand" />
            </multi:listOfSelectorReferences>
          </multi:speciesTypeInstance>

          <multi:SpeciesTypeInstance multi:id="boundligand" multi:initialAmount="0">
            <multi:listOfSelectorReferences>
              <multi:selectorReference multi:selector="sel_complex">
            </multi:listOfSelectorReferences>
          </multi:speciesTypeInstance>
        </multi:listOfSpeciesTypeInstances>
      </species>
    </listOfSpecies>

    <listOfReactions>

<!-- -------------------------------------------------------------------------------- -->
<!-- Phosphorylation of the receptor by the kinase when unbound                       -->
<!-- -------------------------------------------------------------------------------- -->
      <reaction id="phosphorylation" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference species="recept" stoichiometry="1">
            <multi:listOfSpeciesRestriction>
              <multi:speciesRestriction 
                           multi:id="freeRnonP"
                           multi:speciesTypeInstance="freereceptor_nonP" />
            </multi:listOfSpeciesRestriction>
          </speciesReference>
        </listOfReactants>

        <listOfProducts>
          <multi:productSpeciesReference species="recept" stoichiometry="1">
            <multi:listOfSpeciesRestriction>
              <multi:speciesRestriction 
                           multi:id="freeRP"
                           multi:speciesTypeInstance="freereceptor_P" />
            </multi:listOfSpeciesRestriction>
          </multi:productSpeciesReference>
        </listOfProducts>
    
        <listOfModifiers>
          <modifierSpeciesReference species="kinase" />
        </listOfModifiers>

        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML" />
        </kineticLaw>

        <multi:listOfReactionRules>
          <multi:reactionRule multi:id="PhosphorylationUnbound">
            <multi:listOfConditions>
              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="freeRnonP"/>
            </multi:listOfConditions>

            <multi:listOfResults>
              <multi:speciesTypeRestrictionReference multi:speciesTypeRestriction="freeRP"/>
            </multi:listOfResults>

            <kineticLaw>
              <math xmlns="http://www.w3.org/1998/Math/MathML" >
                <apply>
                  <times />
                  <ci> cell </ci>
                  <ci> Vm </ci>
                  <apply>
                    <divide />
                    <ci> recept </ci>
                    <apply>
                      <plus />
                      <ci> recept </ci>
                      <ci> Km </ci>
                    </apply>
                  </apply>
                </apply>
              </math>
 
              <listOfLocalParameters>
                <localParameter id="Km" value="1" />
                <localParameter id="Vm" value="1" />
              </listOfLocalParameters>
            </kineticLaw>
          </multi:reactionRule>
        </multi:listOfReactionRules>
      </reaction>

<!-- -------------------------------------------------------------------------------- -->
<!-- Ligand binding, when the receptor is phosphorylated or not                       -->
<!-- -------------------------------------------------------------------------------- -->
      <reaction id="receptLigBinding" reversible="false" fast="false">
        <listOfReactants>
          <speciesReference id="react_recept" 
                                             species="recept" 
                                             stoichiometry="1">
            <multi:listOfSpeciesRestriction>
              <multi:speciesRestriction 
                           multi:id="freeRnonP"
                           multi:speciesTypeInstance="freereceptor_nonP" />

              <multi:speciesRestriction 
                           multi:id="freeRP"
                           multi:speciesTypeInstance="freereceptor_P" />
            </multi:listOfSpeciesRestriction>
          </speciesReference>

          <speciesReference id="react_lig" 
                                             species="lig" 
                                             stoichiometry="1">
            <multi:listOfSpeciesRestriction>
              <multi:speciesRestriction 
                           multi:id="freeL"
                           multi:speciesTypeInstance="freeligand" />
            </multi:listOfSpeciesRestriction>
          </speciesReference>
        </listOfReactants>

        <listOfProducts>
          <multi:productSpeciesReference 
                       species="recept" stoichiometry="1"
                       correspondingReactant="react_recept">
            <multi:listOfSpeciesRestriction>
              <multi:speciesRestriction 
                           multi:id="boundR"
                           multi:speciesTypeInstance="boundreceptor" />
            </multi:listOfSpeciesRestriction>
          </multi:productSpeciesReference>

          <multi:productSpeciesReference 
                       species="lig" stoichiometry="1"
                       correspondingReactant="react_lig">
            <multi:listOfSpeciesRestriction>
              <multi:speciesRestriction 
                           multi:id="boundL"
                           multi:speciesTypeInstance="boundligand" />
            </multi:listOfSpeciesRestriction>
          </multi:productSpeciesReference>
        </listOfProducts>

        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML" />
        </kineticLaw>

        <multi:listOfReactionRules>
          <multi:reactionRule multi:id="bindingNonPhospho">
            <multi:listOfConditions>
              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="freeRnonP" />

              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="freeL" />
            </multi:listOfConditions>

            <multi:listOfResults>
              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="boundR" />

              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="boundL" />
            </multi:listOfResults>

            <kineticLaw>
              <math xmlns="http://www.w3.org/1998/Math/MathML" >
                <apply>
                  <times />
                  <ci> cell </ci>
                  <ci> kon_nonphos </ci>
                  <ci> recept </ci>
                  <ci> lig </ci>
                </apply>
              </math>

              <listOfLocalParameters>
                <localParameter id="kon_nonphos" value="1">
              </listOfLocalParameters>
            </kineticLaw>
          </multi:reactionRule>

          <multi:reactionRule multi:id="bindingPhospho">
            <multi:listOfConditions>
              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="freeRP" />

              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="freeL" />
            </multi:listOfConditions>

            <multi:listOfResults>
              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="boundR" />

              <multi:speciesTypeRestrictionReference 
                           multi:speciesTypeRestriction="boundL" />
            </multi:listOfResults>

            <kineticLaw>
              <math xmlns="http://www.w3.org/1998/Math/MathML" >
                <apply>
                  <times />
                  <ci> cell </ci>
                  <ci> kon_phos </ci>
                  <ci> recept </ci>
                  <ci> lig </ci>
                </apply>
              </math>

              <listOfLocalParameters>
                <localParameter id="kon_phos" value="10">
              </listOfLocalParameters>
            </kineticLaw>
          </multi:reactionRule>
        </multi:listOfReactionRules>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

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Retrieved from "http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Multistate_and_Multicomponent_Species_Proposal/PhosphoReceptor"

This page was last modified 15:44, 29 November 2010.