Prediction of Interacting Single-Stranded RNA Bases by Protein-Binding Patterns

Alexandra Shulman-Peleg*, Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


Prediction of protein-RNA interactions at the atomic level of detail is crucial for our ability to understand and interfere with processes such as gene expression and regulation. Here, we investigate protein binding pockets that accommodate extruded nucleotides not involved in RNA base pairing. We observed that most of the protein-interacting nucleotides are part of a consecutive fragment of at least two nucleotides whose rings have significant interactions with the protein. Many of these share the same protein binding cavity and more than 30% of such pairs are π-stacked. Since these local geometries cannot be inferred from the nucleotide identities, we present a novel framework for their prediction from the properties of protein binding sites. First, we present a classification of known RNA nucleotide and dinucleotide protein binding sites and identify the common types of shared 3-D physicochemical binding patterns. These are recognized by a new classification methodology that is based on spatial multiple alignment. The shared patterns reveal novel similarities between dinucleotide binding sites of proteins with different overall sequences, folds and functions. Given a protein structure, we use these patterns for the prediction of its RNA dinucleotide binding sites. Based on the binding modes of these nucleotides, we further predict an RNA fragment that interacts with those protein binding sites. With these knowledge-based predictions, we construct an RNA fragment that can have a previously unknown sequence and structure. In addition, we provide a drug design application in which the database of all known small-molecule binding sites is searched for regions similar to nucleotide and dinucleotide binding patterns, suggesting new fragments and scaffolds that can target them.

Original languageEnglish
Pages (from-to)299-316
Number of pages18
JournalJournal of Molecular Biology
Issue number2
StatePublished - 29 May 2008


FundersFunder number
Binational US–Israel Science Foundation
Center for Cancer Research
Hermann Minkowski-MINERVA Center for Geometry
National Institutes of Health1UC1AI067231
National Cancer InstituteNO1-CO-12400, ZIABC010442
National Institute of Allergy and Infectious Diseases
Israel Science Foundation281/05


    • RNA aptamer drug design
    • multiple binding site alignment
    • nucleotide and dinucleotide binding sites
    • physicochemical binding patterns
    • protein-RNA interactions


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