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Structural and biochemical investigation of protein-RNA interactions

Peters, Daniel (2014) Structural and biochemical investigation of protein-RNA interactions. PhD thesis, University of York.

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Abstract

Non-coding RNAs (ncRNAs) are nucleic acids that do not code for protein. Rather, they have evolved highly specialised secondary structures and catalytic mechanisms that place them at the heart of regulating gene expression. The function of ncRNAs is often mediated or dependent on their interactions with RNA binding proteins. The study of both the structure and function of these proteins is crucial for understanding the biological role of the protein-RNA complexes. In this thesis, the structure and function of two RNA binding proteins: Lin28 and dihydrouridine synthase C (DusC) were investigated using X-ray crystallography and biophysical techniques. In both systems, the specific recognition of target molecules is important for function. The aim of the study was therefore to use structural and functional data to elucidate the molecular basis of these protein-RNA interactions. There are three main findings: (1) specific recognition of microRNAs by Lin28 is dependent on the interaction of the Zinc Knuckle domain of the protein with a 3’ GGAG motif; (2) non-specific, electrostatic interactions between the cold-shock domain of Lin28 and RNA suggest a transcriptome scanning mechanism for recognising Lin28 targets; and (3) modification of specific nucleotide positions within tRNA by DusC is dependent on the orientation in which the tRNA is bound, which is determined by minor changes in the protein structure. These findings have helped to elucidate the mechanisms, and hence biological functions, of these RNA binding proteins. Both proteins have been previously associated with cancer. Through greater understanding of the molecular basis of these protein-RNA interactions, the production of novel therapeutic agents can be informed, which can help to combat disease. This data will therefore aid future efforts to treat and prevent the cancers caused by the aberrant actions of these RNA binding proteins.

Item Type: Thesis (PhD)
Keywords: Structural Biology, Biochemistry, Protein, RNA, Cancer, X-ray Crystallography, RNA binding proteins
Academic Units: The University of York > Biology (York)
Identification Number/EthosID: uk.bl.ethos.619087
Depositing User: Mr. Daniel Peters
Date Deposited: 19 Sep 2014 14:38
Last Modified: 24 Jul 2018 15:20
URI: http://etheses.whiterose.ac.uk/id/eprint/6784

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