Multi-Site Conformational Exchange in the Synthetic Neomycin-Sensing Riboswitch Studied by 19F NMR |
| |
Authors: | Jan H Overbeck Jennifer Vögele Felix Nussbaumer Elke Duchardt-Ferner Christoph Kreutz Jens Wöhnert Remco Sprangers |
| |
Institution: | 1. Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93051 Regensburg, Germany;2. Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany;3. Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria |
| |
Abstract: | The synthetic neomycin-sensing riboswitch interacts with its cognate ligand neomycin as well as with the related antibiotics ribostamycin and paromomycin. Binding of these aminoglycosides induces a very similar ground state structure in the RNA, however, only neomycin can efficiently repress translation initiation. The molecular origin of these differences has been traced back to differences in the dynamics of the ligand:riboswitch complexes. Here, we combine five complementary fluorine based NMR methods to accurately quantify seconds to microseconds dynamics in the three riboswitch complexes. Our data reveal complex exchange processes with up to four structurally different states. We interpret our findings in a model that shows an interplay between different chemical groups in the antibiotics and specific bases in the riboswitch. More generally, our data underscore the potential of 19F NMR methods to characterize complex exchange processes with multiple excited states. |
| |
Keywords: | Aminoglycosides 19F NMR NMR Spectroscopy RNA Dynamics |
|
|