Dataset Information

Del_Conte_Zerial2008_Rab5_Rab7_cut_out_switch

ABSTRACT: 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 Biology4:206 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 described mechanism of cargo accumulation. Not explicitly described in the article: activation of Rab5 (time) : r*ke*time/(100+time) /(1+e(kg-R)*kf) instead of r*ke/(1+e(kg-R)*kf) This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.For more information see the terms of use.To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

SUBMITTER: Perla Del Conte-Zerial

PROVIDER: BIOMD0000000174 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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			Action	DRS
	BIOMD0000000174?filename=BIOMD0000000174-biopax2.owl	Owl
	BIOMD0000000174?filename=BIOMD0000000174-biopax3.owl	Owl
	BIOMD0000000174?filename=BIOMD0000000174-matlab.m	Other
	BIOMD0000000174?filename=BIOMD0000000174-octave.m	Other
	BIOMD0000000174?filename=BIOMD0000000174.m	Other

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Membrane identity and GTPase cascades regulated by toggle and cut-out switches.

Del Conte-Zerial Perla P Brusch Lutz L Rink Jochen C JC Collinet Claudio C Kalaidzidis Yannis Y Zerial Marino M Deutsch Andreas A

Molecular systems biology 20080715

Key cellular functions and developmental processes rely on cascades of GTPases. GTPases of the Rab family provide a molecular ID code to the generation, maintenance and transport of intracellular compartments. Here, we addressed the molecular design principles of endocytosis by focusing on the conversion of early endosomes into late endosomes, which entails replacement of Rab5 by Rab7. We modelled this process as a cascade of functional modules of interacting Rab GTPases. We demonstrate that int ...[more]

PMID: 18628746

Publication: 1/3

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