Analysis of interactions between ribosomal proteins and RNA structural motifs.

Détails

ID Serval
serval:BIB_14B0096B0651
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Analysis of interactions between ribosomal proteins and RNA structural motifs.
Périodique
BMC bioinformatics
Auteur(s)
Ciriello G., Gallina C., Guerra C.
ISSN
1471-2105 (Electronic)
ISSN-L
1471-2105
Statut éditorial
Publié
Date de publication
18/01/2010
Peer-reviewed
Oui
Volume
11 Suppl 1
Pages
S41
Langue
anglais
Notes
Publication types: Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Résumé
One important goal of structural bioinformatics is to recognize and predict the interactions between protein binding sites and RNA. Recently, a comprehensive analysis of ribosomal proteins and their interactions with rRNA has been done. Interesting results emerged from the comparison of r-proteins within the small subunit in T. thermophilus and E. coli, supporting the idea of a core made by both RNA and proteins, conserved by evolution. Recent work showed also that ribosomal RNA is modularly composed. Motifs are generally single-stranded sequences of consecutive nucleotides (ssRNA) with characteristic folding. The role of these motifs in protein-RNA interactions has been so far only sparsely investigated.
This work explores the role of RNA structural motifs in the interaction of proteins with ribosomal RNA (rRNA). We analyze composition, local geometries and conformation of interface regions involving motifs such as tetraloops, kink turns and single extruded nucleotides. We construct an interaction map of protein binding sites that allows us to identify the common types of shared 3-D physicochemical binding patterns for tetraloops. Furthermore, we investigate the protein binding pockets that accommodate single extruded nucleotides either involved in kink-turns or in arbitrary RNA strands. This analysis reveals a new structural motif, called tripod. It corresponds to small pockets consisting of three aminoacids arranged at the vertices of an almost equilateral triangle. We developed a search procedure for the recognition of tripods, based on an empirical tripod fingerprint.
A comparative analysis with the overall RNA surface and interfaces shows that contact surfaces involving RNA motifs have distinctive features that may be useful for the recognition and prediction of interactions.
Mots-clé
Binding Sites, Models, Molecular, Nucleic Acid Conformation, Protein Conformation, RNA/chemistry, RNA/metabolism, Ribosomal Proteins/chemistry, Ribosomal Proteins/metabolism
Pubmed
Web of science
Open Access
Oui
Création de la notice
06/07/2018 11:02
Dernière modification de la notice
21/08/2019 5:34
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