Structure-based insights into recognition and regulation of SAM-sensing riboswitches

L Zheng, Q Song, X Xu, X Shen, C Li, H Li… - Science China Life …, 2023 - Springer
Riboswitches are highly conserved RNA elements that located in the 5′-UTR of mRNAs,
which undergo real-time structure conformational change to achieve the regulation of …

The Perturbed Free‐Energy Landscape: Linking Ligand Binding to Biomolecular Folding

AS Abdelsattar, Y Mansour, F Aboul‐ela - ChemBioChem, 2021 - Wiley Online Library
The effects of ligand binding on biomolecular conformation are crucial in drug design,
enzyme mechanisms, the regulation of gene expression, and other biological processes …

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

S Roy, SP Hennelly, H Lammert… - Nucleic acids …, 2019 - academic.oup.com
Investigations of most riboswitches remain confined to the ligand-binding aptamer domain.
However, during the riboswitch mediated transcription regulation process, the aptamer …

Entropy Driving the Mg2+-Induced Folding of TPP Riboswitch RNA

J Li, X Zhang, L Hong, Y Liu - The Journal of Physical Chemistry B, 2022 - ACS Publications
Mg2+ is well known to facilitate the structural folding of RNA. However, the thermodynamic
and dynamic roles of Mg2+ in RNA folding remain elusive. Here, we exploit single-molecule …

Exploring the energy landscape of a SAM-I riboswitch

C Manz, AY Kobitski, A Samanta, K Nienhaus… - Journal of Biological …, 2021 - Springer
SAM-I riboswitches regulate gene expression through transcription termination upon binding
a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the …

Real-time monitoring of the multistate conformational dynamics of polypurine reverse Hoogsteen hairpin to capture their triplex-affinity for gene silencing by smFRET …

D Bandyopadhyay, PP Mishra - The Journal of Physical Chemistry …, 2020 - ACS Publications
Single-molecule Förster resonance energy transfer microspectroscopic methods are
employed for real-time monitoring and to gain deeper insights into the formation of the …

Statistical mechanical prediction of ligand perturbation to RNA secondary structure and application to riboswitches

O Alaidi, F Aboul‐ela - Journal of Computational Chemistry, 2020 - Wiley Online Library
The realization that noncoding RNA is implicated in numerous cellular processes, makes it
imperative to understand and predict RNA‐folding. RNA secondary structure prediction is …

[HTML][HTML] Preface: special topic on single-molecule biophysics

DE Makarov, B Schuler - The Journal of chemical physics, 2018 - pubs.aip.org
Single-molecule measurements are now almost routinely used to study biological systems
and processes. The scope of this special topic emphasizes the physics side of single …

Structural dynamics of eukaryotic H/ACA RNPs from saccharomyces cerevisiae & structural dynamics of the Guanidine-II riboswitch from escherichia coli

C Fuks - 2023 - publikationen.ub.uni-frankfurt.de
Die vorliegende Dissertation mit dem Titel “Structural dynamics of eukaryotic H/ACA RNPs
from Saccharomyces cerevisiae & Structural dynamics of the Guanidine-II riboswitch from …

Modelling the impact of magnesium ions concentration on the folding of the SAM-II riboswitch

O Alaidi - bioRxiv, 2021 - biorxiv.org
Riboswitches are regulatory elements present in bacterial messenger RNA acting as
sensors of small molecules and consequently playing a vital role in bacterial gene …