In- and efflux of antibotics

Abstract

Bacterial resistance against antibiotics is an increasingly important field of study. Since the atomic structure of several influx pores and efflux pumps were resolved recently one now has the possibility to study the structure-function relationship computational via large-scale molecular dynamics (MD) simulations. Both the Italian and the German groups have experience in modelling the influx of ions and antibiotics through cell membranes and now join forces and experience to tackle the more complex problem of efflux pumps. The systems which are in the focus of this investigation do not only transport substrates through one membrane but through the inner as well as the outer membrane of gram-negative bacteria. Because of this the system of study consists of several hundred thousand atoms. The MD code NAMD developed by the Schulten group in Urbana-Champaign which has excellent parallel scaling properties will be used on the DEISA infrastructure to study these very large systems in an European project which would be otherwise impossible. Studying molecular details of the efflux of different antibiotics will help to understand why antibiotics are pumped out of the bacterial cell and therefore are unable to fulfil there task of destroying the cell.