BIOMD0000000174
type: SBMLModel
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
name: Del_Conte_Zerial2008_Rab5_Rab7_cut_out_switch
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
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
modified:
  W3 CDTF: Wed May 16 11:03:39 BST 2012
time units: metaid_0000010
name: Sigmoid Activation
units def: metaid_0000029
reaction: metaid_0000026
created:
  W3 CDTF: Mon Jul 28 13:59:41 BST 2008
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name: extraction
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area units: metaid_0000005
occurs in: http://identifiers.org/taxonomy/9606
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name: hydrolysis
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is: MODEL5937037510
curated: true
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length unit: length
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name: Sigmoid Activation 3 (t)
species: metaid_0000014
is described by: http://identifiers.org/pubmed/18628746
reaction: metaid_0000017
reaction: metaid_0000024
reaction: metaid_0000023
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type: Compartment
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spatial dimensions: 3.0
name: endosomal membrane

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has part: CHEBI:17552

metaid_0000022
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reversible: false
name: activation of Rab7 by GEF5
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