Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
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 Mg 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 Mg and ligand binding.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9300104 | PMC |
| http://dx.doi.org/10.1002/cbic.202100564 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
H, C, N and P chemical shift assignment of the first stem-loop Guanidine-II riboswitch from Escherichia coli.
Biomol NMR Assign
June 2025
Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max‑von‑Laue‑Str. 7, 60438, Frankfurt/M, Germany.
A comprehensive understanding of RNA-based gene regulation is a fundamental aspect for the development of innovative therapeutic options in medicine and for a more targeted response to environmental problems. Within the different mechanisms of RNA-based gene regulation, riboswitches are particularly interesting as they change their structure in response to the interaction with a low molecular weight ligand, often a well-known metabolite. Four distinct classes of riboswitches recognize the very small guanidinium cation.
View Article and Find Full Text PDFCooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch.
NAR Genom Bioinform
September 2024
Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
Riboswitches are involved in regulating the gene expression in bacteria. They are located within the untranslated regions of bacterial messenger RNA and function as switches by adjusting their shape, depending on the presence or absence of specific ligands. To decipher the fundamental aspects of bacterial gene control, it is therefore important to understand the mechanisms that underlie these conformational switches.
View Article and Find Full Text PDFTranslation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity.
RNA
August 2023
Institute of Biochemical Design and Discovery, Yale University, West Haven, Connecticut 06516, USA
Riboswitches function as important translational regulators in bacteria. Comprehensive mutational analysis of transcriptional riboswitches has been used to probe the energetic intricacies of interplay between the aptamer and expression platform, but translational riboswitches have been inaccessible to massively parallel techniques. The guanidine-II (gdm-II) riboswitch is an exclusively translational class.
View Article and Find Full Text PDFCombining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch.
Front Mol Biosci
April 2022
Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany.
Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and electron paramagnetic resonance experiments, an intrastrand kissing loop formation has not been demonstrated.
View Article and Find Full Text PDFCharacterization of Structure and Dynamics of the Guanidine-II Riboswitch from Escherichia coli by NMR Spectroscopy and Small-Angle X-ray Scattering (SAXS).
Chembiochem
February 2022
Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany.
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.
View Article and Find Full Text PDF