Investigations of the Mechanisms and Applications of Pentatricopeptide Repeat (PPR) Proteins
| dc.contributor.advisor | Barkan, Alice | |
| dc.contributor.author | McDermott, James | |
| dc.date.accessioned | 2019-04-30T21:08:13Z | |
| dc.date.issued | 2019-04-30 | |
| dc.description.abstract | Pentatricopeptide repeat proteins (PPR) proteins are helical-repeat proteins that bind RNA in a modular one-nucleotide:one-repeat fashion. The specificity of a given PPR repeat is dictated by amino acids at two-positions, which recognize a particular nucleotide through hydrogen bonds with the Watson-Crick face. The combinations of amino acids at these positions that give rise to nucleotide specificity is referred to as the PPR-code. The modular and programmable nature of PPR proteins makes them promising candidates for use in applications that require targeting a protein to a specific RNA sequence. One mechanism by which PPR proteins act involves the remodeling of inhibitory RNA hairpins that sequester a ribosome binding site upstream of the gene. However, other evidence suggests that PPR protein-RNA interactions can be inhibited by RNA secondary structure. It is not clear what parameters determine which partner prevails in binding to the RNA. I investigated how the position and strength of an RNA structure impacts PPR:RNA binding and determined that even weak RNA structures are able to inhibit PPR:RNA binding. Additionally, I investigated the driving forces of PPR:RNA binding kinetics. Together, these parameters will benefit the design of synthetic PPR proteins for specific purposes. Several groups have demonstrated that synthetic PPR proteins can be designed to bind a specified RNA sequence in vitro. However, no work has been performed using engineered, or designer PPR proteins in an in vivo setting. I demonstrated the feasibility of using a designer PPR protein to bind a specified RNA in vivo, and I applied this capability for a specific application – the purification of an endogenous ribonucleoprotein particle to identify associated proteins. This dissertation contains unpublished co-authored material. | en_US |
| dc.description.embargo | 2021-04-30 | |
| dc.identifier.uri | https://hdl.handle.net/1794/24519 | |
| dc.language.iso | en_US | |
| dc.publisher | University of Oregon | |
| dc.rights | Creative Commons BY 4.0-US | |
| dc.title | Investigations of the Mechanisms and Applications of Pentatricopeptide Repeat (PPR) Proteins | |
| dc.type | Electronic Thesis or Dissertation | |
| thesis.degree.discipline | Department of Chemistry and Biochemistry | |
| thesis.degree.grantor | University of Oregon | |
| thesis.degree.level | doctoral | |
| thesis.degree.name | Ph.D. |
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