Show simple item record

Files in this item

Thumbnail

Item metadata

dc.contributor.advisorMitchell, John B. O.
dc.contributor.advisorBühl, Michael
dc.contributor.authorShrimpton-Phoenix, Eugene
dc.coverage.spatial247en_US
dc.date.accessioned2023-10-30T15:26:15Z
dc.date.available2023-10-30T15:26:15Z
dc.date.issued2023-11-29
dc.identifier.urihttps://hdl.handle.net/10023/28592
dc.description.abstractThe field of study surrounding the PETase class of enzymes has gained a great deal of popularity in the past five years. PETases are enzymes capable of degrading poly(ethylene) terephthalate and presents an opportunity to bioanalytically recycle this common pollutant. The most extensively researched PETase is the enzyme Is-PETase, which originates from the organism Idonella sakaiensis and was discovered near a recycling plant in 2016. To further the utility of Is-PETase in the industrial recycling of poly(ethylene) terephthalate, improvements in desirable properties such as catalytic rate and thermostability must be achieved via introduction of amino-acid substitutions to the enzyme. In order to further improve the activity of Is-PETase, it would be informative to have a deeper understanding of its catalytic mechanism. To this end, we have investigated the catalytic mechanism of the degradation of poly(ethylene) terephthalate via Is-PETase. We applied hybrid quantum mechanical/ molecular mechanical to generate several independent reaction profiles. From these reaction profiles we have concluded that this reaction proceeds with an overall activation barrier of 35.6 kJ mol-1 . This relatively low activation barrier suggests that the ‘true’ rate-limiting step for this reaction is a physical process such as substrate binding or product dissociation. Our calculations provide preliminary evidence for the product dissociation step being rate-limiting. We have also investigated modifications to wild-type Is-PETase that contribute to the enzyme’s thermostability. We have created our own mutant of Is-PETase, DISU-PETase, through the in silico introduction of a novel disulfide bond. We generated reaction profiles for DISU-PETase using the same quantum mechanical/ molecular mechanical techniques as applied to wild-type Is-PETase. We found that introduction of the novel disulfide bond in DISU-PETase had no adverse effect upon the reaction profile of the degradation of poly(ethylene) terephthalate. We have also applied molecular dynamics techniques to investigate the intramolecular interactions that contribute toward the thermostability of the most highly active variants of Is-PETase in the literature. We have also used our quantum mechanical/ molecular mechanical techniques to generate reaction profiles for the degradation of an alternate substrate, poly(ethylene) furanoate via wildtype Is-PETase.en_US
dc.language.isoenen_US
dc.relationComputational Insights into the Catalytic Mechanism of Is-PETase: An Enzyme Capable of degrading poly(ethylene) terephthalate (thesis data) Shrimpton-Phoenix, E., Mitchell, J. B. O., and Buehl, M., University of St Andrews, 27 Oct 2022. DOI: 10.17630/486acc90-3be5-43c2-aa08-17c02096bb85
dc.relation.urihttps://doi.org/10.17630/486acc90-3be5-43c2-aa08-17c02096bb85
dc.subjectEnzymesen_US
dc.subjectQM/MMen_US
dc.subjectPETaseen_US
dc.titleComputational insights into catalytic mechanism and thermostability of the enzyme Is-PETaseen_US
dc.typeThesisen_US
dc.contributor.sponsorEASTbioen_US
dc.type.qualificationlevelDoctoralen_US
dc.type.qualificationnamePhD Doctor of Philosophyen_US
dc.publisher.institutionThe University of St Andrewsen_US
dc.identifier.doihttps://doi.org/10.17630/sta/643
dc.identifier.grantnumberBB/M010996/1en_US


This item appears in the following Collection(s)

Show simple item record