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

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dc.contributor.advisor Williams, Loren D.
dc.contributor.author Hsiao, Chiaolong en_US
dc.contributor.committeeMember Doyle, Donald
dc.contributor.committeeMember Harvey, Stephen
dc.contributor.committeeMember Hud, Nicholas
dc.contributor.committeeMember Wartell, Roger
dc.contributor.department Chemistry and Biochemistry en_US
dc.date.accessioned 2009-01-22T15:52:23Z
dc.date.available 2009-01-22T15:52:23Z
dc.date.issued 2008-08-25 en_US
dc.description.abstract 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. Using PBR analysis, a total of 103 tetraloops within the crystal structures of the 23s rRNA of H. marismortui and the 70s rRNA of T. thermophilus 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. 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 Å, as utilized 73% of RNA backbone atoms (~ 2129 residues). By using principles of inorganic chemistry along with structural alignment technique as described above, a recurrent magnesium-binding motif in large RNAs is revealed. These magnesium-binding motifs play a critical role in the framework of the ribosomal PTC by their locations, topologies, and coordination geometries. Common features of Mg2+-mc's include direct phosphate chelation of two magnesium ions in the form of Mg2+(i)-(O1P-P-O2P)-Mg2+(j), phosphate groups of adjacent RNA residues as ligands of a given Mg2+, and undulated RNA surfaces with unpaired and unstacked bases. en_US
dc.description.degree Ph.D. en_US
dc.identifier.uri http://hdl.handle.net/1853/26634
dc.publisher Georgia Institute of Technology en_US
dc.subject Magnesium-binding motif en_US
dc.subject Superimposition en_US
dc.subject Structural alignment en_US
dc.subject Multiresolution en_US
dc.subject Ribosome en_US
dc.subject Tetraloop en_US
dc.subject.lcsh Bioinformatics
dc.subject.lcsh Ribosomes
dc.subject.lcsh RNA
dc.subject.lcsh Image processing
dc.title Computational bioinformatics on three-dimensional structures of ribosomes using multiresolutional analysis en_US
dc.type Text
dc.type.genre Dissertation
dspace.entity.type Publication
local.contributor.advisor Williams, Loren D.
local.contributor.corporatename School of Chemistry and Biochemistry
local.contributor.corporatename College of Sciences
relation.isAdvisorOfPublication 2886d5c2-dc71-4ca2-a4bf-efd1856ef0aa
relation.isOrgUnitOfPublication f1725b93-3ab8-4c47-a4c3-3596c03d6f1e
relation.isOrgUnitOfPublication 85042be6-2d68-4e07-b384-e1f908fae48a
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