Analysis of interactions between ribosomal proteins and RNA structural motifs

Background: 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 proteinRNA interactions has been so far only sparsely investigated. Results: 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 nucleo...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Giovanni Ciriello, Claudio Gallina, Concettina Guerra
• Keywords: BMCBI 2010, Protein, Ribosomal Rna, RNA Structural Motifs