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Spatial modeling of vesicle transport and the cytoskeleton: the challenge of hitting the right road.

Klann, M. and Koeppl, H. and Reuss, M. (2012):
Spatial modeling of vesicle transport and the cytoskeleton: the challenge of hitting the right road.
In: PloS one, pp. e29645, 7, (1), [Online-Edition: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...],
[Article]

Abstract

The membrane trafficking machinery provides a transport and sorting system for many cellular proteins. We propose a mechanistic agent-based computer simulation to integrate and test the hypothesis of vesicle transport embedded into a detailed model cell. The method tracks both the number and location of the vesicles. Thus both the stochastic properties due to the low numbers and the spatial aspects are preserved. The underlying molecular interactions that control the vesicle actions are included in a multi-scale manner based on the model of Heinrich and Rapoport (2005). By adding motor proteins we can improve the recycling process of SNAREs and model cell polarization. Our model also predicts that coat molecules should have a high turnover at the compartment membranes, while the turnover of motor proteins has to be slow. The modular structure of the underlying model keeps it tractable despite the overall complexity of the vesicle system. We apply our model to receptor-mediated endocytosis and show how a polarized cytoskeleton structure leads to polarized distributions in the plasma membrane both of SNAREs and the Ste2p receptor in yeast. In addition, we can couple signal transduction and membrane trafficking steps in one simulation, which enables analyzing the effect of receptor-mediated endocytosis on signaling.

Item Type: Article
Erschienen: 2012
Creators: Klann, M. and Koeppl, H. and Reuss, M.
Title: Spatial modeling of vesicle transport and the cytoskeleton: the challenge of hitting the right road.
Language: English
Abstract:

The membrane trafficking machinery provides a transport and sorting system for many cellular proteins. We propose a mechanistic agent-based computer simulation to integrate and test the hypothesis of vesicle transport embedded into a detailed model cell. The method tracks both the number and location of the vesicles. Thus both the stochastic properties due to the low numbers and the spatial aspects are preserved. The underlying molecular interactions that control the vesicle actions are included in a multi-scale manner based on the model of Heinrich and Rapoport (2005). By adding motor proteins we can improve the recycling process of SNAREs and model cell polarization. Our model also predicts that coat molecules should have a high turnover at the compartment membranes, while the turnover of motor proteins has to be slow. The modular structure of the underlying model keeps it tractable despite the overall complexity of the vesicle system. We apply our model to receptor-mediated endocytosis and show how a polarized cytoskeleton structure leads to polarized distributions in the plasma membrane both of SNAREs and the Ste2p receptor in yeast. In addition, we can couple signal transduction and membrane trafficking steps in one simulation, which enables analyzing the effect of receptor-mediated endocytosis on signaling.

Journal or Publication Title: PloS one
Volume: 7
Number: 1
Uncontrolled Keywords: Biological, Cell Membrane, Cell Membrane: metabolism, Cell Polarity, Cell Surface, Cell Surface: metabolism, Computer Simulation, Cytoskeleton, Cytoskeleton: metabolism,Endocytosis,Exocytosis,Kinetics,Models,Protein Transport,Receptors,Signal Transduction
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Date Deposited: 04 Apr 2014 12:49
Official URL: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...
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