RNAmap2D

A tool for visualization of 2D maps of RNA structures.

by Natalia Szóstak, Michał J.Piętal, Kristian Rother, Janusz Bujnicki

The resolved structures of RNA highlight the crucial role these molecules play in many biological processes. That is why it is important to extract all the information from the available data; in order to do that it is extremely important to develop new tools and methods for examination of those structures. Two-dimensional maps of distances and contacts between residues in the structure may be useful for many analyses, as the former contain sufficient information to restore the 3D representation, while the latter reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analyses.

What is RNAmap2D

Based on the previous program PROTMAP2D for visualisation of contacts in protein structures, we developed a new tool, RNAMAP2D, dedicated to the analysis of contact maps of RNA structures and protein – RNA complexes. Our program deals with modified base pairs which are very frequent in RNA and includes ligands and ions which plays key roles in forming and stabilizing RNA structures. What is more, it is possible to show on the computed map whether some of the identified contacts are recognized as belonging to one of the 12 base pairs families, are canonical Watson – Crick pairs, or are 4 classes of stacking interactions. The overlap of the 2D maps of two structures can be easily calculated, providing a measure of RNA structure similarity.

RNAmap2D gallery

A rough set calculated for an ensemble code 1JOX. White contacts are those existing in all 24 models while grey color indicates contacts appearing partially so in some models but not in the others.

A simple picture of a RNA-protein CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA (PDB 1DI2). First part of the picture (larger square) is a contact map (CA, 8A) of a complex protein. The remaining part (smaller square) unveils contact map of the RNA structure. Note that group of contacts from rigthmost upper part of the picture (and symmetrical) are those of the protein-RNA interface.

Distance map of the 1EHZ RNA molecule. White color indicates close distance of the basepairs while dark grey pairs are considered spacially distant.

In this picture an example is shown of RNAmap2d coloring capabilities. Panel shown on the right was used here to indicate several types of pairing/ stacking/ other particles. The resulting map is on the left, main part being a 1EHZ RNA molecule, smaller square is a set of ligands and ions contacts, righmost upper (and symmetrical) block indicates contacts between nucleic acid residua and other particles. Note that all kinds of pairings and stacking is determined before the panel is shown thus making some options disabled.

Another 1EHZ structure picture, this time showing only specific contacts that is, any pairings (red), any stacking (green) and any ion or ligand contacts (pink). All the remaining contacts are not shown by setting th colori to black.

The software is expected to be available soon from this location.