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Biophysical and Biochemical Investigation of an Archaeal Box C/D SRNP

Title: Biophysical and Biochemical Investigation of an Archaeal Box C/D SRNP: RNA-Protein Interactions of a Kink Turn RNA within the Functional Enzyme.
Name(s): Moore, Terrie Luong, author
Li, Hong, professor directing dissertation
Epstein, Lloyd M., outside committee member
Logan, Timothy M., committee member
Dorsey, John G., committee member
Department of Chemistry and Biochemistry, degree granting department
Florida State University, degree granting institution
Type of Resource: text
Genre: Text
Issuance: monographic
Date Issued: 2005
Publisher: Florida State University
Florida State University
Place of Publication: Tallahassee, Florida
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: Box C/D snoRNPs catylze the specific 2'O-methylation of rRNA in important regions the ribosome, although the role of the modifications is unclear. Eukaryotic box C/D snoRNPs consists of a box C/D RNA and four proteins, Fibrillarin, Nop56, Nop58, and 15.5kD. Archaeal homologs are simiplified containing three proteins, L7Ae, Nop5p, and Fibrillarin with a box C/D RNA. The box C/D sequences are proposed to form the recently recognized kink turn structure which is found in many types of RNA. Most are associated with proteins and protein binding may nucleate the assembly of other proteins onto the RNA. Dissecting the structure and biochemical properties of box C/D snoRNPs may not only help in understanding the function of the modifications, but may also give insight into the role of kink turn RNAs in RNP assembly. An archaeal box C/D RNA embedded within the intron of pre-tRNATrp from Archaeglobus Fulgidus(AF) that guides two modifications in the tRNA was used as the model for the investigation of three complexes: L7Ae-box C/D RNA, L7Ae-box C'/D' RNA, and the entire box C/D sRNP. Extensive crystallization trials resulted in crystals for each complex. A crystal structure of the box C/D RNA-L7Ae complex was determined to 2.7Å and shows the box C/D sequences do form a kink turn. Detailed structural comparisons of the AF L7Ae-box C/D RNA complex with previously determined crystal structures of L7Ae homologs in complex with functionally distinct kink turn RNAs revealed a conserved RNA-protein interface suggesting a conformational "adaptability" of the kink turn RNAs in binding L7Ae homologs. NMR characterization of L7Ae-box C/D RNA and L7Ae-box C'/D' RNA interactions suggests a structural change in the RNAs upon binding L7Ae and the RNAs may be dynamic structures that do not form stable kink turns alone. The underlying differences in primary and secondary structures of the kink turns may lead to different tertiary structures and dynamic behavior in kink turn RNAs that may confer specificity of L7Ae homologs for different kink turn RNAs. These analyses provide a structural basis for interpreting the functional roles of the box C/D sequences in directing specific assembly of box C/D sRNPs.
Identifier: FSU_migr_etd-2320 (IID)
Submitted Note: A Dissertation Submitted to the Department of Chemistry and Biochemistry in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy.
Degree Awarded: Summer Semester, 2005.
Date of Defense: May 3, 2005.
Keywords: L7Ae, Kink Turn, RNA
Bibliography Note: Includes bibliographical references.
Advisory Committee: Hong Li, Professor Directing Dissertation; Lloyd M. Epstein, Outside Committee Member; Timothy M. Logan, Committee Member; John G. Dorsey, Committee Member.
Subject(s): Chemistry
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Moore, T. L. (2005). Biophysical and Biochemical Investigation of an Archaeal Box C/D SRNP: RNA-Protein Interactions of a Kink Turn RNA within the Functional Enzyme. Retrieved from