ArticleNucleic acids research2012
Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- Therapeutic Potential of Aptamer-Protein Interactions.ACS pharmacology & translational science · 2022Review
- Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.The journal of physical chemistry. B · 2022Article
- Dissecting and predicting different types of binding sites in nucleic acids based on structural information.Briefings in bioinformatics · 2022Article
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions.Life (Basel, Switzerland) · 2021Article
- Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.International journal of molecular sciences · 2020Review
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly.RNA biology · 2019Article
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking.Structure (London, England : 1993) · 2019Article
- Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.Journal of computer-aided molecular design · 2018Article
- Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.RNA (New York, N.Y.) · 2018Article
- 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
- Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands.Angewandte Chemie (International ed. in English) · 2017Article
- Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.Proteins · 2017Article
- Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference.BMC evolutionary biology · 2016Article
- Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.Scientific reports · 2016Article
Corrections and comments
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-RNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the protein surface shape (dented, intermediate or protruded) and the RNA base pairing properties (paired or unpaired nucleotides) at the interfaces of 91 protein-RNA complexes derived from the Protein Data Bank. Dented protein surfaces prefer unpaired nucleotides to paired ones at the interface, and hydrogen bonds frequently occur between the protein backbone and RNA bases. In contrast, protruded protein surfaces do not show such a preference, rather, electrostatic interactions initiate the formation of hydrogen bonds between positively charged amino acids and RNA phosphate groups. Interestingly, in many protein-RNA complexes that interact via an RNA loop, an aspartic acid is favored at the interface. Moreover, in most of these complexes, nucleotide bases in the RNA loop are flipped out and form hydrogen bonds with the protein, which suggests that aspartic acid is important for RNA loop recognition through a base-flipping process. This study provides fundamental insights into the role of the shape of the protein surface and RNA secondary structures in mediating protein-RNA interactions.
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