Student projects - Eefjan Breukink
Plectasin and its variants - Maik Derks
Plectasin is a antimicrobial peptide (AMP) first discovered back in 2005 in the fungus Pseudoplectania nigrella. Plectasin and its variants (e.g. NZ2114, MP1102) have excellent bactericidal activity against a variety of gram positive bacteria. This includes some clinically relevant strains, among which MRSA, infamous in hospitals for causing hard to treat infections. Lipid-II binding is thought to be the mechanism of action of these peptides but much remains unclear about the structural details.
Unfortunately, studying the atomic structure of peptide-Lipid II complexes in their native environment, a membrane, by conventional techniques -such as X-ray diffraction- is challenging. Furthermore, without these data the development of these drugs is like stumbling in the dark, hampering the transition to the clinic of these high-potential candidates. In a collaboration between MBB and the NMR spectroscopy group we study Lipid II binding antibiotics in membranes (or membrane models) by state-of-the-art solid state nuclear magnetic resonance spectroscopy, soon to be supported by the strongest commercial NMR magnet available: 1.2 GHz (expected to be operational in mid-2021).
This is a diverse project, including expression and purification of isotopically labeled peptides, enzymatic/chemical synthesis of Lipid II variants/fluorescent dye analogues, fluorescence spectroscopy, fluorescence microscopy, isothermal calorimetry (ITC), molecular modeling and of course solution/solid state NMR.
Further reading
About Plectasin:
Schneider, T.; Kruse, T.; Wimmer, R.; Wiedemann, I.; Sass, V.; Pag, U.; Jansen, A.; Nielsen, A. K.; Mygind, P. H.; Raventos, D. S.; Neve, S.; Ravn, B.; Bonvin, A. M.; De Maria, L.; Andersen, A. S.; Gammelgaard, L. K.; Sahl, H. G.; Kristensen, H. H., Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II. Science 2010, 328 (5982), 1168-72.
Examples of our research:
Shukla, R.; Medeiros-Silva, J.; Parmar, A.; Vermeulen, B. J. A.; Das, S.; Paioni, A. L.; Jekhmane, S.; Lorent, J.; Bonvin, A. M. J. J.; Baldus, M.; Lelli, M.; Veldhuizen, E. J. A.; Breukink, E.; Singh, I.; Weingarth, M., Mode of action of teixobactins in cellular membranes. Nature Communications 2020, 11 (1), 2848.
Medeiros-Silva, J.; Jekhmane, S.; Paioni, A. L.; Gawarecka, K.; Baldus, M.; Swiezewska, E.; Breukink, E.; Weingarth, M., High-resolution NMR studies of antibiotics in cellular membranes. Nat Commun 2018, 9 (1), 3963.