Thomas E. Exner
Deparment of Chemistry
University of Konstanz

Malte Drescher
Department of Chemistry
University of Konstanz

EPR distance measurement is a relatively new method to analyze 3D structures and dynamics of proteins or nucleic acids. For doing so e.g. two probes with each having an unpaired electron are attached to the protein or nucleic acid and the distance distributions between the unpaired electrons are determined bei EPR spectroscopy. Additionally, extensive MD simulations are performed on the spin-labelled systems to reproduce the distance distributions for test cases, where the 3D structure is known or a small number of possible model structures can be produced. These structural models can then be verified by the agreement between experiment and simulation.

Claudio Anselmi
Max-Planck-Institute für Biophysics, Frankfurt

Wenchang Zhou
Biology Department
Uni-Konstanz

Klaas Martinus Pos
Biology Department
Uni-Frankfurt

Jose Faraldo-Gomez
Max-Planck-Institute for Biophysics, Frankfurt

Kay Diederichs
Biology Department
Uni-Konstanz

Drug resistance during infection or cancer treatment is often caused by the overproduction of efflux transporters inside bacteria, leading to decreased levels of antibiotics or chemotherapeutics inside the cells. This smart machinery inside bacteria is the multidrug-resistance efflux pumps.

AcrB is a major multidrug efflux transporter in E.Coli, which is driven by proton motive force. Recently solved structures confirmed an asymmetric trimer for AcrB, with different orientations in pore domain and helix8 in transmembrane domain, also with key residues involved proton transfer in transmembrane domain. Rotation mechanism proposed based on analysis of the asymmetric structure of AcrB, including Loose (drug access, A), Tight (drug binding, B) and Open (drug extrusion, C), in which also coupled with proton translocations in transmembrane domain.

As we know, a key to understanding how biological systems work is to look at their structures captured in their various functional states. X-ray crystallography is one of the important techniques to determine those states. With excellent jobs from crystallography, now we have several structures for wild type and mutants, which are very helpful to figure out the mechanism employed by AcrB. Because of limitations from crystallography, we still can not find enough functional states which means we need more methods to characterize drug resistance behaviors of AcrB.

Molecular dynamics is the method which we can incorporate to figure out the mechanism employed by AcrB. Although it is a newer and younger experiment on computers relatively to the experiments in the lab, molecular dynamics has already been applied to various fields with the far-reaching development of computer hardware and parallel algorithms. With the help of bwGRiD and the NAMD parallel scalability, we can perform longer molecular dynamics on big systems like AcrB which contains 300,000+ atoms in total.

Tim ten Brink
Theoretische Chemische Dynamik
Fachbereich Chemie
Universtät Konstanz

Thomas Exner
Theoretische Chemische Dynamik
Fachbereich Chemie
Universtät Konstanz

In this project the influence of ligand protonation on docking success rates is systematically studied. On a well defined test set different sets of protonation states are generated for the ligands and the success rate of the dockings is compared to the success rate of either manually refined or fully automatically generated ligand protonation. The protonation states are generated with various methods ranging from purely combinatorial to micro species distribution prediction for a given pH value.