2012 Annual Science Report

Georgia Institute of Technology Reporting  |  SEP 2011 – AUG 2012

RiboVision: Visualization and Analysis of Ribosomes

Project Summary

Ribosomes present special problems and opportunities related to visualization and analysis because they are exceeding complex and information-rich. Many structures have determined at near-atomic resolution, a large number of rRNAs have been sequenced, and each is a large macromolecular assembly with many components and highly complex function. We are devising visualization and analysis methods in analogy with Google Maps, but applied to the ribosome.

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

The RiboEvo team is in the process of developing ‘RiboVision,’ a visualization and analysis tool for simultaneous display of multiple layers of information on primary (1D), secondary (2D), and three-dimensional (3D) representations of ribosomes. RiboVision allows users to easily import and analyze their own data in the context of other work, and to quickly generate publication-quality images of the results. RiboVision has features in rough analogy with Google Maps, Google Earth and Street View, designed for the “Ribosome World.” A long-term goal is to extend this work to support a variety of large macromolecular, geological and astronomical assemblies. Ribovision is available at http://apollo.chemistry.gatech.edu/public/RiboVision.

The ribosome is found in every living cell, and is responsible for translation of genetic information from messenger RNA to coded protein. Ribosomes present special problems and opportunities related to visualization and analysis. Ribosomes are information-rich in that many structures are determined at near-atomic resolution, and each is a large macromolecular assembly with many components and highly complex function. Each ribosome consists of several large ribosomal RNA molecules, over fifty ribosomal proteins, and a large number of cations. A ribosome contains over 300,000 atoms. The structure and function of a ribosome is understood only by consideration of a wide variety of information. Visualization of ribosomes, comparison of sequences, and the mapping of information between dimensions have been cumbersome processes that often required multiple specialized computer tools and manual intervention.

RiboVision currently contains preloaded sequences, alignments, conservation statistics, molecular interactions, and secondary and three-dimensional structures. Data are contained for two bacterial species (Escherichia coli, PDB ID: 3R8N and 3R8S; Thermus thermophilus, PDB IDs: 2J00 and 2J01), one archaeal species (Haloarcula marismortui, PDB ID: 1JJ2), and one eukaryotic species (Saccharomyces, cerevisiae PDB IDs: 3U5B, 3U5C, 3U5D, and 3U5E). Information on both Large and Small Ribosomal subunits is available, except the Small Subunit of H. marismortui, for which no crystal structure is available. RiboVision provides a convenient option for users to upload their own modeling or experimental data, and to project them onto available ribosome structures. User upload templates are available. 3D visualization is integrated via a JMOL web applet.

RiboVision is designed to simultaneously visualize 1D, 2D and 3D structures and to transfer information between them, down to the level of atoms and residues. Available information ranges from base-pairing and molecular interactions, to chemical footprinting, and evolutionary data such as conservation scores (Shannon entropies and nucleotide conservation frequencies). Information relevant to individual residues or linkages between residues can be displayed. Users can select or restrict a certain subset of residues, and the selection is simultaneously made in both 2D and 3D representations.

The display and output of RiboVision uses a layer paradigm, such that many types of data can be displayed and manipulated independently of each other. The 2D data can be activated by selection and projected on demand onto 3D structures. All mapped data can be saved in publication quality PDF, SVG or PNG formats (for 2D), and PML, JPG, or PNG formats for 3D structures.