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AKB: Biologische Physik
AKB 30: Poster Session I
AKB 30.16: Poster
Monday, March 27, 2006, 15:30–18:00, P1
Molecular modeling of transport through OmpF channels — •U. Kleinekathöfer1 and M. Winterhalter2 — 1Institut für Physik, Technische Universität Chemnitz, 09107 Chemnitz — 2International University Bremen, 28725 Bremen
The outer membrane protein F (OmpF) is a non-specific pore in the outer membrane of Escherichia coli and permits translocation of ions and small molecules such as antibiotics [1]. Since the structure of OmpF has been determined to high resolution, it is possible to study the transport through this protein in computer simulations [2,3]. The time-scale problem in simulating the passing of substrate molecules through channels can be overcome by using Steered Molecular Dynamics (SMD) which artificially speeds up the process. This allows to simulate processes on time scales which would not be accessible by an atomic level description otherwise especially diffusive processes. Trajectories obtained from SMD simulations allow to determine the ion current through the protein, its electrostatic map and the potential of mean force.
[1] E. M. Nestorovich, C. Danelon, M. Winterhalter, and S. M. Bezrukov, PNAS 99, 9789 (2002).
[2] K. M. Robertson and D. P. Tieleman, FEBS Lett. 528, 53 (2002).
[3] W. Im and B. Roux, J. Mol. Biol. 319, 1177 (2002).