ArticleRNA biology2015
The role of RNA conformation in RNA-protein recognition.
Article in RNA biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition.bioRxiv : the preprint server for biology · 2026Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease.Molecular biotechnology · 2024Review
- Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.Nature communications · 2024Article
- Chemoproteomic capture of RNA binding activity in living cells.Nature communications · 2023Article
- Roles for theJournal of biological rhythms · 2023Article
- The dynamics of t1 adenosine binding on human Argonaute 2: Understanding recognition with conformational selection.Protein science : a publication of the Protein Society · 2022Article
- Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA.PLoS biology · 2022Article
- The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function.RNA biology · 2022Review
- Review
- Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.International journal of molecular sciences · 2020Review
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
- Structural Changes of RNA in Complex with Proteins in the SRP.Frontiers in molecular biosciences · 2018Review
- Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae.Nucleic acids research · 2017Article
- Article
- Protein-RNA interactions: structural biology and computational modeling techniques.Biophysical reviews · 2016Review
- Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.PLoS computational biology · 2016Article
- MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes.The Journal of biological chemistryArticle
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the structural properties of the RNA at the binding interfaces revealed an unexpected number of nucleotides with unusual RNA conformations, specifically found in RNA-RRM complexes. Moreover, we observed that the RNA nucleotides that are directly involved in interactions with the RRM domains, via hydrogen bonds and hydrophobic contacts, are significantly enriched with unique RNA conformations. Further examination of the sequences binding the RRM domain showed a preference for G nucleotides in syn conformation to precede or to follow U nucleotides in the anti-conformation, and U nucleotides in C2' endo conformation to precede U and G nucleotides possessing the more common C3' endo conformation. These findings imply a possible mode of RNA recognition by the RRM domains which enables the recognition of a wide variety of different RNA sequences and shapes. Overall, this study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout.
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