Berlin 2008 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Posters I

BP 7.35: Poster

Monday, February 25, 2008, 17:00–19:30, Poster A

Simulating an Efflux Pump: Opening the Exit Duct TolC — •Robert Schulz and Ulrich Kleinekathöfer — Jacobs University Bremen, Campus Ring 1, 28759 Bremen,Germany

Bacteria, such as E. coli, use efflux pumps to regulate the permeation of water soluble substances through cell membranes. To allow transport through the outer membrane part of the efflux pump, the so-called TolC, its periplasmic coiled-coil has to be opened [1]. Using all-atom molecular dynamics simulations, including about 200 000 atoms, one is faced with the problem that the conformational changes take place on a timescale far larger than computationally affordable even on today’s supercomputers. Hence, it was investigated whether the opening of TolC and several mutants can be forced by applying an electric field and thereby inducing an extra force by the ions that are solvated in the surrounding water. The rate of opening can easily be traced by calculating the distances of the monomers’ tails from the trimer’s planar center of mass. From the obtained data, ion density, potential maps, and ion currents have been calculated. It is planned to investigate the other constituents of the efflux pump as well.

[1] J. Eswaran, E. Koronakis, M.K. Higgins, C. Hughes, and V. Koronakis, Curr. Op. Struct. Biol. 14, 741 (2004).