Analysis of interactions between ribosomal proteins and RNA structural motifs.

BMC Bioinformatics
Giovanni CirielloConcettina Guerra

Abstract

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 nucleoti...Continue Reading

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Citations

Mar 20, 2012·PloS One·Ajith Harish, Gustavo Caetano-Anollés
Mar 19, 2014·Amino Acids·Michael S ParkerSteven L Parker
Apr 26, 2011·Journal of Molecular Biology·Aditi Gupta, Michael Gribskov
Feb 22, 2012·Molecular Reproduction and Development·Ernest Blackwell, Stephanie Ceman
Nov 12, 2013·Computational Biology and Chemistry·Palak ShethJason T L Wang
Feb 17, 2015·World Journal of Gastroenterology : WJG·Jun-ichi TakinoTakamitsu Hori
May 31, 2018·International Journal of Molecular Sciences·Ambuj SrivastavaM Michael Gromiha
Oct 13, 2018·Synthetic Biology·Tim WeeninkTom Ellis

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