Poster abstracts

Poster number 127 submitted by Poorna Roy

Automated detection and classification of RNA-protein interactions

Poorna Roy (Center for Photochemical Sciences, Bowling Green State University), Blake A. Sweeney (Department of Biology, Bowling Green State University), Neocles B. Leontis (Center for Photochemical Sciences, Bowling Green State University)

Abstract:
RNA-protein interactions play crucial roles in all stages of transcription, translation and gene regulation. RNA-binding proteins interact specifically with RNA molecules using a variety of non-covalent interactions to achieve exquisite binding selectivity, including: (i) electrostatic interactions between fully ionized groups, (ii) hydrogen bonding, (iii) and hydrophobic interactions, such as aromatic stacking. Very often, the same amino acid makes two or more interactions with a single or neighboring nucleotides, thus increasing sensitivity. Such multiple inter-molecular contacts correspond to recurrent binding motifs, some of which have been previously described (Kondo and Westhof, 2011). For example, base and amino-acid specific “pseudo-pairs” result when a single amino acid forms two or more H-bonds with an RNA base. In the course of this work, new pseudo-pairs involving histidine interacting in the RNA minor groove were identified, as well as bidentate interactions in which a single amino acid H-bonds to two stacked RNA bases. As it is important to systematically detect and annotate these these non-covalent interactions to make them searchable in databases, we have developed programs, integrated into the RNA.BGSU.EDU and NDB data pipeline to provide RNA-protein interaction annotations that can be searched symbolically or geometrically. The interactions that are annotated will be illustrated and statistical surveys of the occurrences of these interactions in current releases of NDB will be presented.

References:
Kondo, J and Westhof, E. (2011) “Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes”. Nucleic Acids Res. 2011, 1-10.

Keywords: RNA-protein, Annotation, Database