Robert Schulz

• Multidrug resistance against antibiotics is a common problem of treating bacterial infections. One of the major contributors are efflux pumps, that reduce the periplasmic concentration of antibiotics and other toxic compounds by pumping them out into the extracellular space. This thesis comprises several computational approaches to investigate the functions of the individual proteins of Escherichia coli's major efflux pump AcrAB-TolC. In the first part, the opening of the periplasmic tip of TolC, an outer-membrane channel, was investigated by mutating specific residues in this region as it was shown in X-ray crystal structures. Upon docking to one of several possible inner-membrane transporters, TolC is supposed to open iris-likely. In the present simulations, this opening was accomplished to a similar extent as in experiments. In the second part, the dynamics of AcrB's pumping process have been investigated by mimicking conformational changes which have been proposed by X-ray crystallographers. The outcome has been described by using a drug molecule as an unbiased measure. During this investigation, the binding pocket has been found to shrink peristaltically, which forced the drug to leave the binding pocket. In a subsequent work, the influence of its environment has been examined. Especially the interaction with the surrounding water and amino acids revealed several essential features of the extrusion by AcrB. One interesting aspect was the stream of water which slightly assisted the extrusion of the drug and also shielded the electrostatic interaction of the protein and the substrate. This disfavored a strong binding of the drug to the amino acids of the exit channel. Furthermore, the inter- and intramonomeric interactions have been examined and crucial conformational changes of the transition along the cycle have been highlighted. The effect of one particular mutation on the extrusion has been investigated in an additional work. The information presented in this thesis enhances the atomistic and functional understanding of E. coli's major efflux pump. By combining these data with experimental results, the mechanism of extrusion can be interpreted more clearly, which might also improve the chances to develop new antibiotics and inhibitors with a higher efficacy in the future.