Rad5 Replication Fork Rescue Mechanism Elucidation with a Structural Perspective

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dc.contributor.advisorVlassakis, Juleaen_US
dc.contributor.advisorGao, Yangen_US
dc.creatorMolina Limon, Noelen_US
dc.date.accessioned2025-01-17T17:25:26Zen_US
dc.date.created2024-12en_US
dc.date.issued2024-12-06en_US
dc.date.submittedDecember 2024en_US
dc.date.updated2025-01-17T17:25:26Zen_US
dc.description.abstractStalled replication forks are frail structures with exposed single stranded (ss) DNA regions that are prone to digestion breaks. These are highly cytotoxic and energetically expensive to repair. Organisms have systems in place to protect and resolve stalled forks so replication can continue. Failure with said systems is closely associated with cell death and cancer. Fork reversal is a rescue mechanism for stalled replication forks that as the name implies, relies on re-zipping of the opened parental strand until a four-way double stranded intermediate is obtained. Helicase-like Transcription Factor (HLTF) in humans, and its low eukaryote ortholog Rad5, are prime examples of fork reversal enzymes. Interest in HLTF and its role in oncogenesis has been hampered by the complexity of expressing and manipulating this frail enzyme. Despite the hurdles, understanding the fork reversal mechanism is critical to identify how organisms discern between rescue events and disease progression. Exploiting the thermally resilient proteome of C. thermophilum, and functional homolog Rad5, allowed the study and elucidation of mechanistic details of enzyme-mediated fork reversal. Validation of Rad5 from a non-model organism exhibited the advantages of thermally stable enzymes and cements the future   use of alternatives to overcome physical and logistical issues that plague recombinant enzyme production. Concerted biochemical and structural studies were performed to gain mechanistic information on Rad5 reversal of the replication fork. Our findings showed a regulatory effect by the enzyme’s distal n-terminal domain, that is linked to substrate specificity. Our work also identified the strand Rad5 translocating of DNA occurs on, which further solidifies our hypothesized mechanism and counters the enzyme’s historical description as an annealing helicase. Finally sample optimization and complex formation studies lay the groundwork for continuing structural tests.en_US
dc.embargo.lift2025-06-01en_US
dc.embargo.terms2025-06-01en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.urihttps://hdl.handle.net/1911/118238en_US
dc.language.isoenen_US
dc.subjectreplication forken_US
dc.subjectreplication fork reversalen_US
dc.subjectannealing helicaseen_US
dc.subjectRad5en_US
dc.subjectSnf2en_US
dc.subjectc. thermophilumen_US
dc.subjectHLTFen_US
dc.titleRad5 Replication Fork Rescue Mechanism Elucidation with a Structural Perspectiveen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentBioengineeringen_US
thesis.degree.disciplineBioengineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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