Abstract
The RNA Bricks database (http://iimcb.genesilico.pl/rnabricks), stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA–protein complexes. In contrast to other similar tools (RNA 3D Motif Atlas, RNA Frabase, Rloom) RNA motifs, i.e. ‘RNA bricks’ are presented in the molecular environment, in which they were determined, including RNA, protein, metal ions, water molecules and ligands. All nucleotide residues in RNA bricks are annotated with structural quality scores that describe real-space correlation coefficients with the electron density data (if available), backbone geometry and possible steric conflicts, which can be used to identify poorly modeled residues. The database is also equipped with an algorithm for 3D motif search and comparison. The algorithm compares spatial positions of backbone atoms of the user-provided query structure and of stored RNA motifs, without relying on sequence or secondary structure information. This enables the identification of local structural similarities among evolutionarily related and unrelated RNA molecules. Besides, the search utility enables searching ‘RNA bricks’ according to sequence similarity, and makes it possible to identify motifs with modified ribonucleotide residues at specific positions.
Highlights
Folded RNA molecules exhibit hierarchical organization. They are composed of modular units, in particular regularly shaped double-stranded helices formed by ribonucleotide residues paired in the Watson–Crick (WC) sense, and irregularly shaped motifs formed by residues engaged in various non-WC interactions
We introduce a specific definition of an ‘RNA brick’ as a set of interacting nucleotide residues from the same chain, flanked by WC or wobble base pairs
RNA bricks are listed in interactive tables that display sequence and secondary structure data, local quality scores and contact information (Figure 2A)
Summary
Examples of structural motifs include kink-turn [1], sarcin–ricin motif [2], p-turn [3] and t-loop [4,5] These motifs usually have complex internal structures, and they participate in interactions of high biological significance. They often introduce precise kinks and turns of the RNA backbone that position adjacent helices with respect to each other, and they mediate specific intra-molecular contacts that induce the compact folding of mediumsized and large RNAs [6]. The understanding of RNA structure– function relationships depends critically on the identification and classification of the motifs, both in terms of their internal structure and with respect to the molecules they interact with
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