ArticleNucleic acids research2014
Hydration of protein-RNA recognition sites.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 39 citations in OpenAlex.
- Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition.Current research in structural biology · 2026Article
- RNApedia: a database of structural protein-RNA interactions.Frontiers in bioinformatics · 2026Article
- Marginal Stability of the YB1 Cold-Shock Domain in Cells Enables Binding of Multiple Nucleic Acids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions.Journal of molecular biology · 2025Article
- Water-mediated ribonucleotide-amino acid pairs and higher-order structures at the RNA-protein interface: analysis of the crystal structure database and a topological classification.NAR genomics and bioinformatics · 2024Article
- Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments.Journal of the American Chemical Society · 2024Article
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs.FEBS open bio · 2019Article
- PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees.Frontiers in genetics · 2019Article
- Review
- An account of solvent accessibility in protein-RNA recognition.Scientific reports · 2018Article
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
- Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Nucleic acids research · 2017Article
- Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces.BMC bioinformatics · 2017Article
- Protein-RNA interactions: structural biology and computational modeling techniques.Biophysical reviews · 2016Review
- Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.Scientific reports · 2016Article
- Probing binding hot spots at protein-RNA recognition sites.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively 'dry' than interfaces with tRNA and duplex RNA. In contrast to protein-DNA interfaces, mainly due to the presence of the 2'OH, the ribose in protein-RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein-RNA interfaces is hydrated more than the major groove, while in protein-DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein-RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein-RNA recognition and should be carefully treated while engineering protein-RNA interfaces.
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