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<?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 name="E-cadherin_mediated_adhesion">
<!-- Definitions -->
<listOfUnitDefinitions>
<unitDefinition id="litre_per_mole_per_sec">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1" />
<unit kind="mole" exponent="-1" scale="0" multiplier="1" />
<unit kind="second" exponent="-1" scale="0" multiplier="1" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="micron_square_per_sec">
<listOfUnits>
<unit kind="metre" exponent="2" scale="-6" multiplier="1" />
<unit kind="second" exponent="-1" scale="0" multiplier="1" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="micrometre_per_sec">
<listOfUnits>
<unit kind="metre" exponent="1" scale="-6" multiplier="1" />
<unit kind="second" exponent="-1" scale="0" multiplier="1" />
</listOfUnits>
</unitDefinition>
<unitDefinition id="per_sec">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="1" />
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<!-- Compartments -->
<listOfCompartments>
<compartment id="membrane" constant="true" multi:isType="true" />
<compartment id="inter_membrane" constant="true" multi:isType="true">
<multi:listOfCompartmentReferences>
<multi:compartmentReference multi:id="m1" multi:compartment="membrane" />
<multi:compartmentReference multi:id="m2" multi:compartment="membrane" />
</multi:listOfCompartmentReferences>
</compartment>
</listOfCompartments>
<!-- SpeciesTypes -->
<multi:listOfSpeciesTypes>
<!-- Ecad with cis-binding site and trans-binding site: -->
<multi:bindingSiteSpeciesType multi:id="st_Cis_Interface" />
<multi:bindingSiteSpeciesType multi:id="st_Trans_Interface" />
<multi:speciesType multi:id="st_Ecad" multi:compartment="membrane">
<multi:listOfSpeciesTypeInstances>
<multi:speciesTypeInstance multi:id="cis" multi:speciesType="st_Cis_Interface" />
<multi:speciesTypeInstance multi:id="trans" multi:speciesType="st_Trans_Interface" />
</multi:listOfSpeciesTypeInstances>
</multi:speciesType>
<!-- cis dimer: -->
<multi:speciesType multi:id="st_Ecad_cis_dimer" multi:compartment="membrane">
<multi:listOfSpeciesTypeInstances>
<multi:speciesTypeInstance multi:id="Ecad1" multi:speciesType="st_Ecad" />
<multi:speciesTypeInstance multi:id="Ecad_2" multi:speciesType="st_Ecad" />
</multi:listOfSpeciesTypeInstances>
<multi:listOfSpeciesTypeComponentIndexes>
<multi:speciesTypeComponentIndex multi:id="Ecad1cis"
multi:component="cis" multi:identifyingParent="Ecad1" />
<multi:speciesTypeComponentIndex multi:id="Ecad2cis"
multi:component="cis" multi:identifyingParent="Ecad2" />
<multi:speciesTypeComponentIndex multi:id="Ecad1trans"
multi:component="trans" multi:identifyingParent="Ecad1" />
<multi:speciesTypeComponentIndex multi:id="Ecad2trans"
multi:component="trans" multi:identifyingParent="Ecad2" />
</multi:listOfSpeciesTypeComponentIndexes>
<multi:listOfInSpeciesTypeBonds>
<multi:inSpeciesTypeBond multi:bindingSite1="Ecad1cis"
multi:bindingSite2="Ecad2cis" />
</multi:listOfInSpeciesTypeBonds>
</multi:speciesType>
<!-- trans dimer: -->
<multi:speciesType multi:id="st_Ecad_trans_dimer" multi:compartment="inter_membrane">
<multi:listOfSpeciesTypeInstances>
<multi:speciesTypeInstance multi:id="Ecad1" multi:speciesType="st_Ecad"
multi:compartmentReference="m1" />
<multi:speciesTypeInstance multi:id="Ecad2" multi:speciesType="st_Ecad"
multi:compartmentReference="m2" />
</multi:listOfSpeciesTypeInstances>
<multi:listOfSpeciesTypeComponentIndexes>
<multi:speciesTypeComponentIndex multi:id="Ecad1trans"
multi:component="trans" multi:identifyingParent="Ecad1" />
<multi:speciesTypeComponentIndex multi:id="Ecad2trans"
multi:component="trans" multi:identifyingParent="Ecad2" />
<multi:speciesTypeComponentIndex multi:id="Ecad1cis"
multi:component="cis" multi:identifyingParent="Ecad1" />
<multi:speciesTypeComponentIndex multi:id="Ecad2cis"
multi:component="cis" multi:identifyingParent="Ecad2" />
</multi:listOfSpeciesTypeComponentIndexes>
<multi:listOfInSpeciesTypeBonds>
<multi:inSpeciesTypeBond multi:bindingSite1="Ecad1trans"
multi:bindingSite2="Ecad2trans" />
</multi:listOfInSpeciesTypeBonds>
</multi:speciesType>
<!-- trimer: -->
<multi:speciesType multi:id="st_Ecad_trimer" multi:compartment="inter_membrane">
<multi:listOfSpeciesTypeInstances>
<multi:speciesTypeInstance multi:id="Ecad1" multi:speciesType="st_Ecad"
multi:compartmentReference="m1" />
<multi:speciesTypeInstance multi:id="Ecad2" multi:speciesType="st_Ecad"
multi:compartmentReference="m1" />
<multi:speciesTypeInstance multi:id="Ecad3" multi:speciesType="st_Ecad"
multi:compartmentReference="m2" />
</multi:listOfSpeciesTypeInstances>
<multi:listOfSpeciesTypeComponentIndexes>
<multi:speciesTypeComponentIndex multi:id="Ecad1cis"
multi:component="cis" multi:identifyingParent="Ecad1" />
<multi:speciesTypeComponentIndex multi:id="Ecad1trans"
multi:component="trans" multi:identifyingParent="Ecad1" />
<multi:speciesTypeComponentIndex multi:id="Ecad2cis"
multi:component="cis" multi:identifyingParent="Ecad2" />
<multi:speciesTypeComponentIndex multi:id="Ecad2trans"
multi:component="trans" multi:identifyingParent="Ecad2" />
<multi:speciesTypeComponentIndex multi:id="Ecad3cis"
multi:component="cis" multi:identifyingParent="Ecad3" />
<multi:speciesTypeComponentIndex multi:id="Ecad3trans"
multi:component="trans" multi:identifyingParent="Ecad3" />
</multi:listOfSpeciesTypeComponentIndexes>
<multi:listOfInSpeciesTypeBonds>
<multi:inSpeciesTypeBond multi:bindingSite1="Ecad1cis"
multi:bindingSite2="Ecad2cis" />
<multi:inSpeciesTypeBond multi:bindingSite1="Ecad1trans"
multi:bindingSite2="Ecad3trans" />
</multi:listOfInSpeciesTypeBonds>
</multi:speciesType>
</multi:listOfSpeciesTypes>
<!-- Species -->
<listOfSpecies>
<!-- free Ecad -->
<species id="sp_Ecad_unbound" name="Ecad_unbound" compartment="membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="cis"
multi:bindingStatus="unbound" />
<multi:outwardBindingSite multi:component="trans"
multi:bindingStatus="unbound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad trans unbnd -->
<species id="sp_Ecad_trans_unbnd" name="Ecad_trans_unbnd" compartment="membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="trans"
multi:bindingStatus="unbound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad trans bnd -->
<species id="sp_Ecad_trans_bnd" name="Ecad_trans_bnd" compartment="membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="trans"
multi:bindingStatus="bound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad all -->
<species id="sp_Ecad_all" name="Ecad_all" compartment="membrane"
hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false" multi:speciesType="st_Ecad" />
<!-- Pattern species: Ecad cis unbnd -->
<species id="sp_Ecad_cis_unbnd" name="Ecad_cis_unbnd" compartment="membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="cis"
multi:bindingStatus="unbound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad cis unbnd, trans bnd -->
<species id="sp_Ecad_6" name="Ecad_6" compartment="membrane" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false" multi:speciesType="st_Ecad">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="cis"
multi:bindingStatus="unbound" />
<multi:outwardBindingSite multi:component="trans"
multi:bindingStatus="bound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad cis bnd, trans unbnd -->
<species id="sp_Ecad_7" name="Ecad_7" compartment="membrane" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false" multi:speciesType="st_Ecad">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="cis"
multi:bindingStatus="bound" />
<multi:outwardBindingSite multi:component="trans"
multi:bindingStatus="unbound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad cis dimer -->
<species id="sp_Ecad_cis_dimer" name="Ecad_cis_dimer" compartment="membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad_cis_dimer" />
<!-- Pattern species: Ecad cis dimer: all trans bnd -->
<species id="sp_EcadEcad_2" name="Ecad.Ecad_2" compartment="membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad_cis_dimer">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="Ecad1trans"
multi:bindingStatus="bound" />
<multi:outwardBindingSite multi:component="Ecad2trans"
multi:bindingStatus="bound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad trans dimer -->
<species id="sp_EcadEcad_1" name="Ecad.Ecad_1" compartment="inter_membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad_trans_dimer" />
<!-- Pattern species: Ecad trans dimer: all cis bnd -->
<species id="sp_Ecad_trans_dimer_2" name="Ecad_trans_dimer_2" compartment="inter_membrane"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"
multi:speciesType="st_Ecad_trans_dimer">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="Ecad1cis"
multi:bindingStatus="bound" />
<multi:outwardBindingSite multi:component="Ecad2cis"
multi:bindingStatus="bound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad True Trimer -->
<species id="sp_Ecad_True_Trimer" compartment="inter_membrane" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false" multi:speciesType="st_Ecad_trimer">
<multi:listOfOutwardBindingSites>
<multi:outwardBindingSite multi:component="Ecad2trans"
multi:bindingStatus="unbound" />
<multi:outwardBindingSite multi:component="Ecad3cis"
multi:bindingStatus="unbound" />
</multi:listOfOutwardBindingSites>
</species>
<!-- Pattern species: Ecad All Trimer -->
<species id="sp_Ecad_All_Trimer" compartment="inter_membrane" hasOnlySubstanceUnits="false"
boundaryCondition="false" constant="false" multi:speciesType="st_Ecad_trimer" />
</listOfSpecies>
<!-- Reactions -->
<listOfReactions>
<!-- cis association: -->
<reaction id="rc_Cis_Association" name="Cis_Association" reversible="false" fast="false"
compartment="membrane">
<listOfReactants>
<speciesReference id="Cis_Association_r1" species="sp_Ecad_6"
stoichiometry="1" constant="false" />
<speciesReference id="Cis_Association_r2" species="sp_Ecad_6"
stoichiometry="1" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference species="sp_EcadEcad_2" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> kon </ci>
<ci multi:speciesReference="Cis_Association_r1"> sp_Ecad_6 </ci>
<ci multi:speciesReference="Cis_Association_r2"> sp_Ecad_6 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kon" value="9000" units="litre_per_mole_per_sec" />
</listOfLocalParameters>
</kineticLaw>
</reaction>
<!-- In species cis association: Here the model requires that the two interacting molecules
are part of one connected complex already prior to the association. Since the necessary
connectivity can only be mediated by the trans binding sites here, these sites must be
bound to the subcomplex (not shown) linking the two interacting molecules.
-->
<multi:intraSpeciesReaction id="rc_Intra_Complex_Cis_Association"
name="Intra-Complex_Cis_Association"
reversible="false" fast="false" compartment="membrane">
<listOfReactants>
<speciesReference id="Intra_Complex_Cis_Association_r1" species="sp_Ecad_6"
stoichiometry="1" constant="false" />
<speciesReference id="Intra_Complex_Cis_Association_r2" species="sp_Ecad_6"
stoichiometry="1" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference species="sp_EcadEcad_2" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> kon </ci>
<ci multi:speciesReference="Intra_Complex_Cis_Association_r1"> sp_Ecad_6 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kon" value="100" units="per_sec" />
</listOfLocalParameters>
</kineticLaw>
</multi:intraSpeciesReaction>
<!-- trans association: -->
<reaction id="rc_Trans_Association" name="Trans_Association" reversible="false" fast="false"
compartment="inter_membrane">
<listOfReactants>
<speciesReference id="Trans_Association_r1" species="sp_Ecad_trans_unbnd"
multi:compartmentReference="m1" constant="false" />
<speciesReference id="Trans_Association_r2" species="sp_Ecad_trans_unbnd"
multi:compartmentReference="m2" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference species="sp_EcadEcad_1" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> kon </ci>
<ci multi:speciesReference="Trans_Association_r1"> sp_Ecad_trans_unbnd </ci>
<ci multi:speciesReference="Trans_Association_r2"> sp_Ecad_trans_unbnd </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kon" value="90000" units="litre_per_mole_per_sec" />
</listOfLocalParameters>
</kineticLaw>
</reaction>
<!-- In complex trans association: Here the model requires that the two interacting molecules
are part of one connected complex already prior to the association. Since the necessary
connectivity can only be mediated by the cis binding sites here, these sites must be bound
to the subcomplex (not shown) linking the two interacting molecules.
-->
<multi:intraSpeciesReaction id="rc_Intra_Complex_Trans_Association"
name="Intra-Complex_Trans_Association"
reversible="false" fast="false" compartment="inter_membrane" >
<listOfReactants>
<speciesReference id="Intra_Complex_Trans_Association_r1" species="sp_Ecad_7"
multi:compartmentReference="m1" constant="false" />
<speciesReference id="Intra_Complex_Trans_Association_r2" species="sp_Ecad_7"
multi:compartmentReference="m2" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference species="sp_Ecad_trans_dimer_2" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> kon </ci>
<ci multi:speciesReference="Intra_Complex_Trans_Association_r1"> sp_Ecad_7 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kon" value="100" units="per_sec" />
</listOfLocalParameters>
</kineticLaw>
</multi:intraSpeciesReaction>
<!-- cis dissociation: -->
<reaction id="rc_Cis_dissociation" name="Cis_dissociation" reversible="false" fast="false"
compartment="membrane">
<listOfReactants>
<speciesReference species="sp_Ecad_cis_dimer" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference id="Cis_dissociation_p1" species="sp_Ecad_cis_unbnd"
stoichiometry="1" constant="false" />
<speciesReference id="Cis_dissociation_p2" species="sp_Ecad_cis_unbnd"
stoichiometry="1" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> koff </ci>
<ci> sp_Ecad_cis_unbnd </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="koff" value="1" units="per_sec" />
</listOfLocalParameters>
</kineticLaw>
</reaction>
<!-- In-species cis dissociation: By specifying that this reaction breaks only an inner bond,
the model limits the application of this reaction to dissociations that result in only one
reaction product. The complex is still connected through a subcomplex that is not shown
here but that links the two molecules involved in the reaction at their trans binding
sites. Note that the modeler application has to ensure the correct application of this
rule and its consistent definition. For instance, specifying the one or both of the trans
binding sites to be unbound would lead to a rule that could never be applied because the
trans bindings are required for the connectivity of the result complex.
-->
<multi:intraSpeciesReaction id="rc_Intra_Complex_Cis_dissociation"
name="Intra-Complex_Cis_dissociation"
reversible="false" fast="false" compartment="membrane" >
<listOfReactants>
<speciesReference species="sp_EcadEcad_2" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference id="Intra_Complex_Cis_dissociation_p1" species="sp_Ecad_6"
stoichiometry="2" constant="false" />
<speciesReference id="Intra_Complex_Cis_dissociation_p2" species="sp_Ecad_6"
stoichiometry="2" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> koff </ci>
<ci> sp_Ecad_6 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="koff" value="0.01" units="per_sec" />
</listOfLocalParameters>
</kineticLaw>
</multi:intraSpeciesReaction>
<!-- trans dissociation: -->
<reaction id="rc_Trans_dissociation" name="Trans_dissociation" reversible="false"
fast="false" compartment="inter_membrane">
<listOfReactants>
<speciesReference species="sp_EcadEcad_1" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference id="Trans_dissociation_p1" species="sp_Ecad_trans_unbnd"
multi:compartmentReference="m1" constant="false" />
<speciesReference id="Trans_dissociation_p2" species="sp_Ecad_trans_unbnd"
multi:compartmentReference="m2" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> koff </ci>
<ci> sp_Ecad_trans_unbnd </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="koff" value="1" units="per_sec" />
</listOfLocalParameters>
</kineticLaw>
</reaction>
<!-- In species trans dissociation: By specifying that this reaction breaks only an inner
bond, the model limits the application of this reaction to dissociations that result in
only one reaction product. The complex is still connected through a subcomplex that is
not shown here but that links the two molecules involved in the reaction at their cis
binding sites. Note that the modeler application has to ensure the correct application
of this rule and its consistent definition. For instance, specifying the one or both of
the cis binding sites to be unbound would lead to a rule that could never be applied
because the cis bindings are required for the connectivity of the result complex.
-->
<multi:intraSpeciesReaction id="rc_Intra_Complex_Trans_dissociation"
name="Intra-Complex_Trans_dissociation"
reversible="false" fast="false" compartment="inter_membrane" >
<listOfReactants>
<speciesReference species="sp_Ecad_trans_dimer_2" constant="false" />
</listOfReactants>
<listOfProducts>
<speciesReference id="Intra_Complex_Trans_dissociation_p1" species="sp_Ecad_7"
multi:compartmentReference="m1" constant="false" />
<speciesReference id="Intra_Complex_Trans_dissociation_p2" species="sp_Ecad_7"
multi:compartmentReference="m2" constant="false" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times />
<ci> koff </ci>
<ci> sp_Ecad_7 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="koff" value="0.01" units="per_sec" />
</listOfLocalParameters>
</kineticLaw>
</multi:intraSpeciesReaction>
</listOfReactions>
</model>
</sbml>
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