Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions

Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Motivation: Understanding the details of protein-RNA interactions is important to reveal the functions of both the RNAs and the proteins. In these interactions, the secondary structures of the RNAs play an important role. Because RNA secondary structures in protein-RNA complexes are variable, considering the ensemble of RNA secondary structures is a useful approach. In particular, recent studies have supported the idea that, in the analysis of RNA secondary structures, the base-pairing probabilities (BPPs) of RNAs (i.e. the probabilities of forming a base pair in the ensemble of RNA secondary structures) provide richer and more robust information about the structures than a single RNA secondary structure, for example, the minimum free energy structure or a snapshot of structures in the Protein Data Bank. However, there has been no investigation of the BPPs in protein-RNA interactions. Results: In this study, we analyzed BPPs of RNA molecules involved in known protein-RNA complexes in the Protein Data Bank. Our analysis suggests that, in the tertiary structures, the BPPs (which are computed using only sequence information) for unpaired nucleotides with intermolecular hydrogen bonds (hbonds) to amino acids were significantly lower than those for unpaired nucleotides without hbonds. On the other hand, no difference was found between the BPPs for paired nucleotides with and without intermolecular hbonds. Those findings were commonly supported by three probabilistic models, which provide the ensemble of RNA secondary structures, including the McCaskill model based on Turner's free energy of secondary structures. Contact: iwakiri@cb.k.u-tokyo.ac.jp or mhamada@cb.k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)2524-2528
Number of pages5
JournalBioinformatics
Volume29
Issue number20
DOIs
Publication statusPublished - 2013 Oct 15
Externally publishedYes

Fingerprint

RNA Secondary Structure
RNA
Pairing
Base Pairing
Molecules
Proteins
Protein
Hydrogen Bonds
Interaction
Ensemble
Secondary Structure
Free Energy
Nucleotides
Hydrogen
Hydrogen bonds
Tokyo
Snapshot
Probabilistic Model
Free energy
Amino Acids

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. / Iwakiri, Junichi; Kameda, Tomoshi; Asai, Kiyoshi; Hamada, Michiaki.

In: Bioinformatics, Vol. 29, No. 20, 15.10.2013, p. 2524-2528.

Research output: Contribution to journalArticle

Iwakiri, Junichi ; Kameda, Tomoshi ; Asai, Kiyoshi ; Hamada, Michiaki. / Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. In: Bioinformatics. 2013 ; Vol. 29, No. 20. pp. 2524-2528.
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