RNAmap2Da tool for visualization of 2D maps of RNA structures

by Michał J. Piętal, Natalia Szóstak, Kristian Rother and Janusz M. 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.

 

RNAmap2D v. 1.7.5, a major update for Linux, Windows and MacOSX is available at this ftp location.  Windows and OSX versions are now standalone programs.  Before installing the program on other platform, please refer to README and User's Manual documents.

 

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.

Technical Notice:  Because since the software was originally built and published, a number of Linux/BSD and macOS systems were made available, the respective target builds may no longer be supported.  Thus in order to use the program, we encourage the users to use either the Windows build natively or launch one with the use of Wine / Darwine frameworks (https://www.winehq.org , http://darwine.sourceforge.net ), under most recent Linux/BSD or macOS flavours, respectively.  These auxiliary tools been mentioned are freeware and easily installable, so no additional license or substantial effort is needed.


Please cite:


Pietal, M. J., Szostak, N., Rother, K. M., & Bujnicki, J. M. (2012). RNAmap2D–calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. BMC bioinformatics, 13(1), 333.
 

 

RNAmap2D gallery
 

A rough set calculated for an ensemble code 1JOX (left). White contacts are those existing in all 24 models while grey colour indicates contacts appearing partially so in some models but not in the others. please note that RNA secondary structure was computed and displayed (pink and violet dots). The 3D structure is shown on the right.

 

A picture of an RNA-protein complex: double-stranded RNA binding domain of S. cerevisiae RNAse III in complex with an AAGU tetraloop hairpin (PDB 2LBS, model 1). 3D structure is shown below the contact map. First part of the picture (larger square, shown in yellow) is a contact map (all-atom metric, 3.5 A) of complex-containing protein. The remaining part (smaller square, shown in blue) unveils contact map within the RNA structure (all-atom metric, 3.5 A). Note that group of contacts from rightmost upper part of the picture (and symmetrically, shown in orange) are those of the protein-RNA interface. Colour bars within protein section indicate secondary structure: red (helix) and green (strand), RNA secondary structure is present in this picture as well.

 

Distance map of the 1EHZ RNA molecule. Normally, ligand and ion pseudochain is also present (see: below), but the user can choose specific chains for the purpose of final map calculation. White colour indicates close distance of the base pairs while dark grey pairs are considered spatially distant. 3D structure is also shown.

 

In this picture an example is shown of RNAmap2D colouring 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, rightmost 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 the colour to black.