Bacteria will always find ways to defend themselves against substances such as antibiotics, thus inhibiting their effect. Many bacteria have pump systems that they use to actively remove antibiotic drugs from the cell. Prof. Kay Diederichs at the University of Constance is working on the elucidation of these mechanisms in order to produce useful information for the development of bacterial pump inhibitors.
The first penicillin-resistant bacteria were found only three years after mass production of the antibiotic, which was discovered in 1928, had begun. While some of the bacterial target proteins, such as DNA gyrase or ribosomes, mutate to prevent antibiotics from binding to bacterial cell structures, the bacteria's pump systems are also effective protective barriers against antibiotics. E. coli bacteria, which, amongst other things, remove the bile salt from human intestines, also have such antibiotics expellers. Working with Prof. Klaas M. Pos from the University of Frankfurt, Kay Diederichs has discovered that E. coli bacteria use an antibiotic pump system (AcrB) with a peristaltic mechanism to trap and expel antibiotics from the cell. "The expression of such pumps will be augmented where antibiotics are present, making the bacteria highly resistant to a broad range of antibiotics," said Kay Diederichs.
The E. coli AcrB pump has three components: a substrate/proton antiporter in the inner membrane, a channel in the outer membrane and a membrane fusion protein between the two membranes. “All three components need to be fully functional for the pump to work efficiently. Defects in one of the three components result in a considerable decrease in resistance to antibiotics,” said Diederichs. Bacterial pump systems are characterised by a broad substrate specificity, i.e. the ability of the pumps to trap and extrude structurally very different molecules, including antibiotics, detergents, dyes or organic solvents from the cell. “Our focus is centred on the structural and biochemical investigation of the AcrB transporter, which is of key importance in the bacteria’s substrate specificity and in the energetisation of the transport,” said Kay Diederichs.
Over the last few years, Diederichs and his team have succeeded in gaining a high-resolution X-ray structure of the transporter in an asymmetric conformation, which led the researchers to suggest a completely new transport mechanism, in which the substrate glides through the individual tunnel-shaped monomers. The antibiotics molecule, which enters a bacterial cell, is trapped by the AcrB pump and glides through the tunnel. “In the same way as food is transported in the oesophagus, the antibiotic is expelled from the pump through peristaltic movements,” explained Prof. Kay Diederichs. Once the antibiotic has left the tunnel, the AcrB transport protein closes the tunnel exit and re-opens the tunnel entrance, thereby enabling the bacteria to expel several antibiotics molecules one after the other from the cell. The elucidation of the structure of AcrB has provided Kay Diederichs and Klaas M. Pos with important insights into how AcrB pumps utilise proton electrochemical gradients to energize the efflux of antibiotics and other compounds out of the bacterial cell. The researchers were surprised to find that AcrB has a similar “functional rotation” to another important membrane protein, the F1F0 ATPase. In terms of medical application, Diederichs’ research shows that the antibiotics pump system is often the cause of postoperative infections that cannot be treated with traditional antibiotics. This discovery is helping the researcher to develop effective remedies.
Kay Diederichs:Kay Diederichs received his PhD from the Faculty of Chemistry and Pharmacy at the University of Freiburg in 1990 for his work on the "X-ray structure analysis of two crystal forms of adenylate kinase found in bovine heart mitochondria". He spent a postdoctoral period at Cornell University (Ithaka, New York) during which he worked on the structural investigation of the cytokine "granulocyte-colony stimulating factor". In 1999, Kay Diederichs habilitated at the University of Constance on the structural analysis of proteins with a special focus on "porins of the outer bacterial membrane". Diederichs has been professor of molecular bioinformatics at the University of Constance since 2004. He started his research on AcrB in 2001.
AcrB has parallels with human proteins such as the Niemann-Pick C1 (NPC1) protein which is associated with the transport of cholesterol across the endosomal/lysosomal membrane. NPC disease is a neurodegenerative disorder that often leads to death in early adolescence. Insights into the energy coupling between the electrochemical gradients and the transport of substances with AcrB are of great importance in helping the researchers to understand the transport mechanism of Niemann-Pick C1 or patched transporters. Asked about his future goals, Diederichs explained that his team hopes to find out “the paths the protons take and how the translocation of protons is translated into mechanical power”. “This alters the conformation of the periplastic binding domain, resulting in the transport of substrate,” said the structural biologist from Constance, also pointing out their intention to work with industrial partners who could use the structure of AcrB to construct inhibitors, for example.