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Exploring the energy landscape of a SAM-I riboswitch

Manz, Christoph; Kobitski, Andrei Yu; Samanta, Ayan; Nienhaus, Karin; Jäschke, Andres; Nienhaus, Gerd Ulrich

Abstract:
SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg$^{2+}$ and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-L-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg$^{2+}$ concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. ... mehr


Verlagsausgabe §
DOI: 10.5445/IR/1000139762
Veröffentlicht am 12.11.2021
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Angewandte Physik (APH)
Institut für Nanotechnologie (INT)
Institut für Biologische und Chemische Systeme (IBCS)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2021
Sprache Englisch
Identifikator ISSN: 0092-0606, 1573-0689
KITopen-ID: 1000139762
HGF-Programm 43.32.02 (POF IV, LK 01) Designed Optical Materials
Erschienen in Journal of Biological Physics
Verlag Springer
Band 47
Seiten 371–386
Vorab online veröffentlicht am 26.10.2021
Nachgewiesen in Scopus
Web of Science
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