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Cellular translocation of biomolecules using ratcheting dynamics.
Description of the project:- no english description available -Runtime:
The translocation of biopolymers through nanopores is known to be a crucial process in cellular biology (Ambjörnsson, T., M. A. Lomholt, and R. Metzler. Directed motion emerging from two coupled random processes: translocation of a chain through a membrane nanopore driven by binding proteins. J. of Physics: Condensed matter 17, S3945-S3964, 2005). Such processes have been modelled by means of a "Brownian ratchet" (Peskin, C. S., G. M. Odell, and G. F. Oster. Cellular motions and thermal fluctuations: The Brownian ratchet. Biophys. J. 65, 316-324, 1993). In such models, diffusion through the nanopore occures by thermal fluctuations. In addition, target sites at the translocated biomolecule prevent movement of the biomolecule from the lumen back to the cytosol. Such target sites are often assumed to be fixed positions of the translocated biomolecule. However, as described by Liebermeister et al. (Ratcheting in post-translational protein translocation: A mathematical model. J. Mol. Biol. 305, 643-656, 2001), the translocation of proteins into the Endoplasmatic Reticulum (ER) is based on the random binding of an ATPase to the protein inside the ER lumen. Thus the movement of the protein into the ER depends on the process of binding and unbinding of ATPases. We study such Brownian ratchets under realistic scenarios.
Additional information: http://www.stochastik.uni-freiburg.de
Phone: 0761/203-5667
Email: peter.pfaffelhuber@stochastik.uni-freiburg.de
Start of project: 01.04.2008Project Management:
End of project: 31.12.2009
Albert-Ludwigs-University Freiburg
Prof. Dr. Peter Pfaffelhuber
Abteilung für Mathematische Stochastik
Prof. Dr. Peter Pfaffelhuber
Ernst-Zermelo-Straße 1
79104 Freiburg
Germany
Phone: 0761/203-5664
Fax: 0761/203-5661
Email: sekretariat@stochastik.uni-freiburg.de
http://www.stochastik.uni-freiburg.de/pfaffelhuber
Actual Research Report
Contributors:
- Depperschmidt A
- BMBF (FRISYS)
- Depperschmidt A, Pfaffelhuber P: Asymptotics of a Brownian ratchet for Protein Translocation. Stochastic Processes and Their Applications, 2010; 120: 901-925. : http://arxiv.org/abs/0904.2276v2 (download: http://arxiv.org/abs/0904.2276v2)