Dresden 2009 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 12: Single Molecules

BP 12.12: Vortrag

Mittwoch, 25. März 2009, 13:00–13:15, HÜL 186

Transport through OmpF channels simulated using molecular dynamics — •Soroosh Pezeshki, Mathias Winterhalter, and Ulrich Kleinekathöfer — Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany

The outer membrane porin OmpF is one of the major porins in E. coli and is the main entrance for small molecules like beta-lactam antibiotics. The narrowest part of the pore, the constriction zone, includes charged residues which have a high but still not well understood influence on the ion permeation. Here different mutations of OmpF are used to study the influence of charged residues on the conductance [1]. The selectivity of the pore can be changed over wide ranges by mutations. In a second step the translocation of antibiotics molecules through the pore is simulated. To speed up the translocation steered molecular dynamics (SMD) is employed. Different pulling strategies are used to get a better understanding of the interaction of pore and antibiotics. The SMD simulations are compared to so-called meta-dynamics simulations for calculating the potential of mean force (PMF) and at the same time used to analyze in vitro experiments [2].

[1] C. Chimerel and L. Movileanu and S. Pezeshki and M. Winterhalter and U. Kleinekathöfer, 2008, Eur. Biophys. J., 38, 121-125

[2] C. Danelon and E. M. Nestorovich and M. Winterhalter and M. Ceccarelli and S. M. Bezrukov, 2006, Biophys. J., 90,1617-1617