Characterization of Structure and Dynamics of the Guanidine-II Riboswitch from Escherichia coli by NMR Spectroscopy and Small-Angle X-ray Scattering (SAXS).
Tatjana SchamberOliver BinasAndreas SchlundtAnna WackerHarald SchwalbePublished in: Chembiochem : a European journal of chemical biology (2021)
Riboswitches are regulatory RNA elements that undergo functionally important allosteric conformational switching upon binding of specific ligands. The here investigated guanidine-II riboswitch binds the small cation, guanidinium, and forms a kissing loop-loop interaction between its P1 and P2 hairpins. We investigated the structural changes to support previous studies regarding the binding mechanism. Using NMR spectroscopy, we confirmed the structure as observed in crystal structures and we characterized the kissing loop interaction upon addition of Mg2+ and ligand for the riboswitch aptamer from Escherichia coli. We further investigated closely related mutant constructs providing further insight into functional differences between the two (different) hairpins P1 and P2. Formation of intermolecular interactions were probed by small-angle X-ray scattering (SAXS) and NMR DOSY data. All data are consistent and show the formation of oligomeric states of the riboswitch induced by Mg2+ and ligand binding.
Keyphrases
- high resolution
- escherichia coli
- transcription factor
- atomic force microscopy
- electronic health record
- molecular dynamics simulations
- magnetic resonance
- big data
- dual energy
- small molecule
- mass spectrometry
- single molecule
- magnetic resonance imaging
- klebsiella pneumoniae
- sensitive detection
- ionic liquid
- binding protein
- machine learning
- monte carlo
- quantum dots
- deep learning
- electron microscopy