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dc.contributor.advisorMitchell, John B. O.
dc.contributor.authorAlderson, Rosanna Grace
dc.coverage.spatial200 p.en_US
dc.date.accessioned2017-03-20T14:10:19Z
dc.date.available2017-03-20T14:10:19Z
dc.date.issued2016-06-22
dc.identifieruk.bl.ethos.707259
dc.identifier.urihttp://hdl.handle.net/10023/10496
dc.description.abstractTracking the evolution of function in enzyme superfamilies is key in understanding how important biological functions and mechanisms have evolved. New genes are being sequenced at a rate that far surpasses the ability of characterization by wet-lab techniques. Moreover, bioinformatics allows for the use of methods not amenable to wet lab experimentation. We now face a situation in which we are aware of the existence of many gene families but are ignorant of what they do and how they function. Even for families with many structurally and functionally characterized members, the prediction of function of ancestral sequences can be used to elucidate past patterns of evolution and highlight likely future trajectories. In this thesis, we apply in silico structure and function methods to predict the functions of protein sequences from two diverse superfamily case studies. In the first, the metallo-β-lactamase superfamily, many members have been structurally and functionally characterised. In this work, we asked how many times the same function has independently evolved in the same superfamily using ancestral sequence reconstruction, homology modelling and alignment to catalytic templates. We found that in only 5% of evolutionary scenarios assessed, was there evidence of a lactam hydrolysing ancestor. This could be taken as strong evidence that metallo-β-lactamase function has evolved independently on multiple occasions. This finding has important implications for predicting the evolution of antibiotic resistance in this protein fold. However, as discussed, the interpretation of this statistic is not clear-cut. In the second case study, we analysed protein sequences of the DUF-62 superfamily. In contrast to the metallo-β-lactmase superfamily, very few members of this superfamily have been structurally and functionally characterised. We used the analysis of alignment, gene context, species tree reconciliation and comparison of the rates of evolution to ask if other functions or cellular roles might exist in this family other than the ones already established. We find that multiple lines of evidence present a compelling case for the evolution of different functions within the Archaea, and propose possible cellular interactions and roles for members of this enzyme family.en_US
dc.language.isoenen_US
dc.publisherUniversity of St Andrews
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectEvolutionen_US
dc.subjectEnzymeen_US
dc.subjectFunctionen_US
dc.subjectSuperfamiliesen_US
dc.subjectPhylogeneticsen_US
dc.subjectAncestral sequence reconstructionen_US
dc.subjectHomology modelingen_US
dc.subjectBioinformaticsen_US
dc.subjectSequence alignmenten_US
dc.subjectDrug discoveryen_US
dc.subject.lccQP601.A63
dc.subject.lcshEnzymesen
dc.subject.lcshMolecular eveolutionen
dc.subject.lcshDrugs--Designen
dc.titleTracking the evolution of function in diverse enzyme superfamiliesen_US
dc.typeThesisen_US
dc.contributor.sponsorBiotechnology and Biological Sciences Research Council (BBSRC)en_US
dc.type.qualificationlevelDoctoralen_US
dc.type.qualificationnamePhD Doctor of Philosophyen_US
dc.publisher.institutionThe University of St Andrewsen_US


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