ArticleScientific reports2018
An account of solvent accessibility in protein-RNA recognition.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
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- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
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- Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response.Molecular biotechnology · 2024Article
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- Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins.PLoS computational biology · 2022Article
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
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- Complementarity of the residue-level protein function and structure predictions in human proteins.Computational and structural biotechnology journal · 2022Article
- NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae.Quantitative plant biology · 2022Article
- Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing.Nucleic acids research · 2021Article
- Structural alterations in the catalytic core of hSIRT2 enzyme predict therapeutic benefits ofRSC advances · 2021Article
- Single Molecule Measurements of the Accessibility of Molecular Surfaces.Frontiers in molecular biosciences · 2021Article
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- Review
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2 authors.
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Abstract
Protein-RNA recognition often induces conformational changes in binding partners. Consequently, the solvent accessible surface area (SASA) buried in contact estimated from the co-crystal structures may differ from that calculated using their unbound forms. To evaluate the change in accessibility upon binding, we compare SASA of 126 protein-RNA complexes between bound and unbound forms. We observe, in majority of cases the interface of both the binding partners gain accessibility upon binding, which is often associated with either large domain movements or secondary structural transitions in RNA-binding proteins (RBPs), and binding-induced conformational changes in RNAs. At the non-interface region, majority of RNAs lose accessibility upon binding, however, no such preference is observed for RBPs. Side chains of RBPs have major contribution in change in accessibility. In case of flexible binding, we find a moderate correlation between the binding free energy and change in accessibility at the interface. Finally, we introduce a parameter, the ratio of gain to loss of accessibility upon binding, which can be used to identify the native solution among the flexible docking models. Our findings provide fundamental insights into the relationship between flexibility and solvent accessibility, and advance our understanding on binding induced folding in protein-RNA recognition.
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