Biophysics

• Nanopore as sensing elements: Biological mesoscopic channels selectively allow small molecules like nutrients to membranes. We characterize the movement of small molecules across a biological channel at the level of a single molecule. This principle can also be used for detection and discriminating between single Dand L- amino acid substitution. Here, our ultimate goal is to sequence peptides or proteins. 
• Antibiotic uptake in Gram-negative bacteria: Within the Innovative Medicine Initiative, the European Union set up a larger platform called New Drugs for Bad Bugs (www.ND4BB.eu) to support the development of new antibiotics. The Constructor University team was academic leader of the Translocation, a subgroup which involved up to 150 researchers from 28 institutions in Europe and overseas. The project was a private-public partnership with five major pharmaceutical companies bringing in a number of basic questions concerning the current bottlenecks in antibiotic development. In a joint effort, we investigated how to overcome the poor permeability of antibiotics acting against Gram-negative bacteria. Outer membranes are often a rate-limiting step for antibiotics. Chemical optimisation, informed by the permeability properties of lead molecules, can help an antibiotic enter a specific area, and may enhance its antimicrobial activity. In the Translocation group, we developed experimental methods to quantify permeability parameters. Using a toolbox of experimental and in-silico methods, we investigated a wide range of mechanisms that allow antibiotics to pass through membranes, and in future researchers can systematically apply these findings to create optimized compounds. The Translocation consortium provided technologies which address multiple transport mechanisms, such as porins, siderophore uptake systems, and efflux systems. Its results will help to expose targets located in all cellular compartments to antibiotic compounds.

• We quantified cephalosporin uptake in vivo vs. in model system.
• We discriminated between a single D-L conversation in a small peptide.
• We published a review of our antibiotic uptake investigation.
• We investigated the influence of LPS on transport and enhanced detection by chemical modification.
• We had a weekly webinar — nanoporemeeting2020 — which had between 60 and 120 participants.

The group currently comprises nine researchers, and projects are funded by BMBF-JPIAMR (Reset-Me and Translocation-Transfer a Virtual Institute), BMBF (TSenArEO).

• M Masi, J Vergalli, I Ghai, A Barba-Bon, T Schembri, WM Nau, D Lafitte, M Winterhalter, JM Pagès. Cephalosporin translocation across enterobacterial OmpF and OmpC channels, a filter across the outer membrane. Comm. Biology 5 (2022) 1059. 
• J Wang, JD Prajapati, F Gao, Ying, U Kleinekathöfer, M Winterhalter, Yi-Tao Long. Identification of single amino acid chiral and positional isomers using an electrostatically asymmetric nanopore. Journal of the American Chemical Society 144 (2022) 15072-78. 
• JD Prajapati, U Kleinekathöfer, M Winterhalter. How to enter a bacterium: bacterial porins and the permeation of antibiotics. Chemical Reviews 121 (2021), 5158-5192. 
• J Wang, R Terrasse, JA Bafna, L Benier, M Winterhalter. Electrophysiological Characterization of Transport Across Outer-Membrane Channels from Gram-Negative Bacteria in Presence of Lipopolysaccharides. Angewandte Chemie International Edition 59 (2020), 8517-8521. 
• J Wang, JA Bafna, SP Bhamidimarri, M Winterhalter. Small-Molecule Permeation across Membrane Channels: Chemical Modification to Quantify Transport across OmpF. Angewandte Chemie International Edition 58 (2019), 4737- 4741.