Computational bioinformatics on three-dimensional structures of ribosomes using multiresolutional analysis.

This thesis presents my work on deciphering, exploring, and discovering the treasure troves of RNA structural bioinformatics, mainly in the areas of multi-resolution analysis of RNA structure. RNA is amazing. We found that without changing the backbone connectivity, RNA can maintain structural conservation in 3D via topology switches, at a single residue level. I developed a method of representing RNA structure in multiresolution, called the PBR approach (P stands for Phosphate; B stands for Base; R stands for Ribose). In this method, structural data is viewed through a series of resolutions from finest to coarsest. At a single nucleotide resolution (fine resolution), RNA is abstruse and elaborate with structural insertions/deletions, strand clips, and 3,2-switches. The compilation of structural deviations of RNA, called DevLS (Deviations of Local Structure), provides a new descriptive language of RNA structure, allowing one to systematize and investigate RNA structure. At PBR resolution (coarse resolution), fundamental RNA architecture, e.g. A-helix, tetraloop, Kink-turns, E-loop motifs etc., becomes readily observable. Using PBR analysis, a total of 103 tetraloops within the crystal structures of the 23s rRNA of H. marismortui (PDB entry: 1JJ2) and the 70s rRNA of T. thermophilus (PDB entry: 2J00 and 2J01) are found and classified. Combining them, I constructed a 'tetraloop family tree', using a tree formalism, to unify and re-define the tetraloop motif and to represent relationships between tetraloops, as grouped by DevLS. To date, structural alignment of very large RNAs remains challenge due to the large size, intricate backbone choreography, and tertiary interactions. To overcome these obstacles, I developed a concept of structural anchors along with a 'Divide and Conquer' strategy for performing superimposition of 23s rRNAs. Here I use tetraloops as structural anchors. The successful alignment and superimpositions of the 23s rRNAs of T. thermophilus and H. marismortui gives an overall RMSD of atomic positions of 1.2 A. This superimposition utilizes 73% of RNA backbone atoms (around 2129 residues). This accurate superimposition allows me to identify regions of structural conservation and diversity, to determine relationships between structural and sequence variation, and to investigate structural relationships between RNA to RNA, RNA to ions, ions to ions, at atomic resolution. By using principles of inorganic chemistry along with structural alignment technique as described above, a recurrent magnesium-binding motif in large RNAs (the 23S rRNAs from H. marismortui and T. thermophilus , the P4-P6 domain of the tetrahymena Group I intron ribozyme, and a Group II intron ribozyme) is revealed. These magnesium-binding motifs play a critical role in the framework of the Peptidyl Transferase Center of the ribosome by their locations, topologies, and coordination geometries. Features of magnesium-binding motif include (i) bridging phosphate chelation of two magnesium ions in the form of Mg2+(i)-(O1P-P-O2P)-Mg 2+(j), (ii) 10-membered chelation ringsutilizing phosphate groups of adjacent residues as Mg2+ ligands, (iii) crystalline-like Mg2+-Mg2+ proximities, (iv) direct Mg2+-phosphate interactions and Mg2+ dehydration, (v) undulated RNA surfaces with unpaired and unstacked bases, and (vi) and usually, close proximity to site of catalysis.