Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 89, P. 102937 - 102937
Published: Oct. 19, 2024
Language: Английский
International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(19), P. 10682 - 10682
Published: Oct. 4, 2024
Riboswitches are highly structured RNA regulators of gene expression. Although found in all three domains life, they particularly abundant and widespread bacteria, including many human pathogens, thus making them an attractive target for antimicrobial development. Moreover, the functional versatility riboswitches to recognize a myriad ligands, ions, amino acids, diverse small-molecule metabolites, has enabled generation synthetic aptamers that have been used as molecular probes, sensors, regulatory devices. Generally speaking, riboswitch consists ligand-sensing aptamer domain expression platform, whose genetic control is achieved through formation mutually exclusive secondary structures ligand-dependent manner. For most riboswitches, this involves aptamer’s P1 helix regulation its stability, competing structure turns ON/OFF at level transcription or translation. Structural knowledge conformational changes involving helix, therefore, essential understanding structural basis ligand-induced switching. This review provides summary cases which ligand-free ligand-bound determined. Comparative analyses these illustrate uniqueness not only ligand sensing but also various mechanisms achieve same end regulating switch stability. In cases, stabilizes primarily coaxial stacking interactions promote helical continuity.
Language: Английский
Citations
4
Proteins Structure Function and Bioinformatics, Journal Year: 2025, Volume and Issue: unknown
Published: April 9, 2025
ABSTRACT We introduce an updated non‐redundant protein‐RNA docking benchmark version 3.0 (PRDBv3.0) containing 197 test cases curated from 288 unique protein–RNA complexes available in the Protein Data Bank until July 2024. Among these, 27 are unbound–unbound (UU) type where both binding partners their unbound states, 160 unbound–bound (UB) only protein is state and remaining 10 bound–unbound (BU) RNA state. The categorized into three classes based on conformational flexibility of interface: 117 rigid‐body (R) with minimal structural changes, 41 semi‐flexible (S) showing moderate changes 29 full‐flexible (F) significant changes. current represents a 62% increase number compared to its previous version. Binding affinity ( K d ) values for subset 105 PRDBv3.0 catalogued along additional experimental details develop comprehensive benchmark. Moreover, total 255 RNA‐binding domains, present proteins, also this will facilitate evaluation flexible methods as well that aim predict affinity. freely at http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php .
Language: Английский
Citations
0
Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 89, P. 102937 - 102937
Published: Oct. 19, 2024
Language: Английский
Citations
0