820986
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000025
kinetic law: 821180
product: 821168
reactant: 821155
is version of: GO:0003924
fast: false
reversible: false
name: hydrolysis of Rab5 (intr.)
type: Reaction

metaid_0000019
kinetic law: 820948
reactant: 820936
fast: false
reversible: false
name: extraction of Rab5
type: Reaction

330994
units: metaid_0000027
value: 0.1
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821204
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species: metaid_0000015
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820838
exponent: 1.0
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331016
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value: 0.15
type: LocalParameter

821034
stoichiometry: 1.0
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820789
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metaid_0000026
kinetic law: 821216
product: 821204
reactant: 821192
is version of: GO:0003924
fast: false
reversible: false
name: hydrolysis of Rab7 (intr.)
type: Reaction

820886
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

821168
stoichiometry: 1.0
species: metaid_0000013
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331015
units: metaid_0000028
value: 0.06
type: LocalParameter

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value: 3.0
type: LocalParameter

330995
units: metaid_0000031
value: 2.5
type: LocalParameter

821094
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000012
is: GO:0010008
constant: true
size: 1.0
spatial dimensions: 3.0
name: endosomal membrane
type: Compartment

331000
units: dimensionless
value: 3.0
type: LocalParameter

820998
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000027
unit: 820777
unit: 820765
name: M
type: SBMLUnitsDef

820753
exponent: 1.0
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kind: SECOND
type: SBMLUnit

metaid_0000017
kinetic law: 820874
product: 820862
is version of: GO:0045184
fast: false
reversible: false
name: recruitment of Rab5
type: Reaction

820826
exponent: -1.0
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330999
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821046
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331013
units: metaid_0000028
value: 0.483
type: LocalParameter

metaid_0000018
kinetic law: 820924
modifier: 820911
product: 820898
reactant: 820886
is version of: GO:0032858
fast: false
reversible: false
name: activation of Rab5 (time)
type: Reaction

metaid_0000028
unit: 820789
name: persec
type: SBMLUnitsDef

821082
stoichiometry: 1.0
species: metaid_0000014
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metaid_0000031
unit: 820850
unit: 820838
name: lpermole
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metaid_0000010
unit: 820753
name: sec
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value: 0.483
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value: 0.31
type: LocalParameter

metaid_0000021
reactant: 820986
type: Reaction
product: 820998
is version of: GO:0032858
modifier: 821010
reversible: false
kinetic law: 821022
name: activation of Rab7 by GEF7
fast: false
is version of: GO:0017112

metaid_0000020
kinetic law: 820974
product: 820961
is version of: GO:0045184
fast: false
reversible: false
name: recruitment of Rab7
type: Reaction

metaid_0000029
unit: 820826
unit: 820813
unit: 820801
name: Mpers
type: SBMLUnitsDef

331002
units: metaid_0000028
value: 0.021
type: LocalParameter

metaid_0000015
has part: P51149
in compartment: metaid_0000012
is: GO:0031225
constant: false
has only substance units: false
name: Rab7-GDP
initial concentration: 1.0
initial amount: NaN
boundary condition: false
type: Species
has part: CHEBI:17552

820936
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

331012
units: metaid_0000031
value: 3.0
type: LocalParameter

metaid_0000022
product: 821046
type: Reaction
is version of: GO:0017112
reversible: false
name: activation of Rab7 by GEF5
is version of: GO:0032858
fast: false
reactant: 821034
modifier: 821058
kinetic law: 821070

820862
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

331001
value: 0.1
type: LocalParameter

820801
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000016
initial concentration: 0.001
boundary condition: false
name: Rab7-GTP
initial amount: NaN
in compartment: metaid_0000012
is: GO:0031225
type: Species
has part: CHEBI:15996
has part: P51149
constant: false
has only substance units: false

820765
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

331011
units: metaid_0000027
value: 0.3
type: LocalParameter

330991
units: metaid_0000028
value: 0.3
type: LocalParameter

BIOMD0000000174
name: Del_Conte_Zerial2008_Rab5_Rab7_cut_out_switch
is version of: GO:0032313
compartment: metaid_0000012
function def: metaid_0000004
substance units: metaid_0000003
species: metaid_0000015
notes: Cut-out switch model Membrane identity and GTPase cascades regulated by toggle and cut-out switches Perla Del Conte-Zerial, Lutz Brusch, Jochen C Rink, Claudio Collinet, Yannis Kalaidzidis, Marino Zerial, and Andreas Deutsch: Molecular Systems Biology 4:206 15 July 2008 , doi:10.1038/msb.2008.45 This is the cut-out switch model for the Rab5 - Rab7 transition, also referred to as model 2 in the original publication. This model is not completely described in all details in the publication. Thanks go to Barbara Szomolay and Lutz Brusch for finding and clarifying this. According to Dr. Brusch this model represents the mechanism identified by the qualitative analysis in the article in the scenario deemed most useful by the authors. For the time-course simulations it was necessary to add a time dependency to one of the parameters, which is only verbally described in the article. As argued in the publication the switch between early and late endosomes can be triggered by a parameter change. While with fixed parameter values each switch just converges to one steady state from its initial conditions and stays there, endosomes should switch between two different states. These changes would in reality of course depend on many different factors, such as cargo composition and amount in the specific endosome, its location and some additional cellular control mechanisms and encompass many different parameters. To keep the model simple the authors chose to add a time dependency to only one reaction - ke in the activation of RAB5 is multiplied with a term monotonously increasing over time from 0 to 1. They also hard coded a time dependence in this term, 100 minutes, to make the switch occur after several hundred minutes. As long as this modulating term remains monotonic all resulting time courses should look similar, with the switching behavior depending on the initial conditions and whether the term is increasing or decreasing. Monotonic increase is a reasonable assumption for the …
reaction: metaid_0000022
name: Hills activation
reaction: metaid_0000021
time units: metaid_0000010
type: SBMLModel
name: Sigmoid Activation
created:
  W3 CDTF: Mon Jul 28 13:59:41 BST 2008
units def: metaid_0000029
reaction: metaid_0000026
reaction: metaid_0000025
function def: metaid_0000003
function def: metaid_0000005
modified:
  W3 CDTF: Wed May 16 11:03:39 BST 2012
species: metaid_0000013
species: metaid_0000016
units def: metaid_0000031
name: extraction
units def: metaid_0000027
reaction: metaid_0000018
reaction: metaid_0000020
area units: metaid_0000005
occurs in: http://identifiers.org/taxonomy/9606
reaction: metaid_0000019
name: hydrolysis
volume units: metaid_0000004
is: MODEL5937037510
creator:
  ORG:
    orgname: Center for Information Services and High Performance Computing, University of Technology Dresden, 01062 Dresden, Germany
  n:
    given: Perla
    family: Del Conte-Zerial
curated: true
function def: metaid_0000007
length unit: length
units def: metaid_0000010
name: Sigmoid Activation 3 (t)
species: metaid_0000014
is described by: http://identifiers.org/pubmed/18628746
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
reaction: metaid_0000017
reaction: metaid_0000024
reaction: metaid_0000023
units def: metaid_0000028
function def: metaid_0000006

metaid_0000023
type: Reaction
is version of: GO:0005097
product: 821094
kinetic law: 821118
reactant: 821082
modifier: 821106
is version of: GO:0003924
reversible: false
fast: false
name: hydrolysis of Rab5 by Rab7

330989
units: metaid_0000029
value: 1.0
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820898
stoichiometry: 1.0
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821155
stoichiometry: 1.0
species: metaid_0000014
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metaid_0000013
name: Rab5-GDP
in compartment: metaid_0000012
has only substance units: false
is: GO:0031225
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has part: P20339
has part: CHEBI:17552
type: Species

metaid_0000024
kinetic law: 821143
reactant: 821130
fast: false
reversible: false
name: extraction of rab7
type: Reaction

821192
stoichiometry: 1.0
species: metaid_0000016
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331003
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value: 1.0
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820813
exponent: -1.0
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820850
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kind: MOLE
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metaid_0000014
boundary condition: false
constant: false
in compartment: metaid_0000012
name: Rab5-GTP
initial amount: NaN
has part: P20339
has part: CHEBI:15996
is: GO:0031225
type: Species
has only substance units: false
initial concentration: 0.001

820777
exponent: -1.0
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kind: LITRE
type: SBMLUnit