Combining in silico and in vitro studies on tRNA dynamics and pseudouridine formation by TruB

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dc.contributor.authorFriedt, Jenna
dc.contributor.supervisorWieden-Kothe, Ute
dc.date.accessioned2014-08-29T18:20:18Z
dc.date.available2014-08-29T18:20:18Z
dc.date.issued2013
dc.degree.levelMastersen_US
dc.degree.levelMasters
dc.descriptionix, 134 leaves : ill. (some col.) ; 29 cmen_US
dc.description.abstractRNA is an important molecule in the cell capable of carrying sequence information for protein production and acting as a functional component in essential cellular processes. In order to perform its many roles, RNA must often adopt specific three-dimensional structures that can be stabilized by the introduction of chemical modifications. Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification and is formed by enzymes known as pseudouridine synthases. These enzymes share a common core fold and active site structure, but the exact mechanism of pseudouridine formation is still undetermined. Here, a combination of in silico and in vitro studies were used to identify residues involved in catalysis to better understand the mechanism of pseudouridine formation. Molecular dynamics (MD) simulations of the Escherichia coli pseudouridine synthase TruB, responsible for the formation of the conserved Ψ55 in tRNA, were performed that revealed an interaction network of three active site residues. In vitro mutational studies showed that these residues are not required for substrate binding, but are highly important for catalysis. Additionally, MD simulations of unmodified tRNA were performed to establish a foundation for nucleic acid simulation by monitoring the effect of Mg2+ ions on the stability of tRNA in silico. These simulations will allow for a complex of tRNA and TruB to be simulated in order to complement the experimental studies and better understand the role of protein-RNA interactions. Together, computational and experimental work will assist in determining the mechanism of pseudouridine formation that may be common to all pseudouridine synthases.en_US
dc.identifier.urihttps://hdl.handle.net/10133/3493
dc.language.isoen_CAen_US
dc.proquestyesNoen_US
dc.publisherLethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistryen_US
dc.publisher.departmentDepartment of Chemistry and Biochemistryen_US
dc.publisher.facultyArts and Scienceen_US
dc.relation.ispartofseriesThesis (University of Lethbridge. Faculty of Arts and Science)en_US
dc.subjectTransfer RNA -- Researchen_US
dc.subjectPseudouridine -- Researchen_US
dc.subjectPost-translational modification -- Researchen_US
dc.subjectDissertations, Academicen_US
dc.titleCombining in silico and in vitro studies on tRNA dynamics and pseudouridine formation by TruBen_US
dc.typeThesisen_US
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