Characterization and rational design of biomolecular sensors using molecular dynamics simulations

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dc.contributor.authorSmith, Dustin D.
dc.contributor.authorUniversity of Lethbridge. Faculty of Arts and Science
dc.contributor.supervisorWieden, Hans-Joachim
dc.contributor.supervisorPatel, Trushar R.
dc.date.accessioned2023-07-10T22:11:50Z
dc.date.available2023-07-10T22:11:50Z
dc.date.issued2023
dc.degree.levelPh.D
dc.description.abstractBiosensors are analytical devices that use biological components to detect and report the presence of a target molecule. Although useful for a broad range of purposes, biosensors are conventionally designed using laborious methods limiting development to a small number of applications with large commercial value. To overcome this limitation, computational approaches are needed to streamline rational design of protein-fluorophore conjugate-type biosensors. Here, I report and iteratively improve such a biosensor development pipeline based on protein molecular dynamics simulations, exploiting underlying dynamic properties of proteins for biosensor design. As proof-of-concept, I report the construction of several carbohydrate-detecting biosensors which are advantageous compared to previous carbohydrate detection methods, and I use these biomolecular tools to characterize several Carbohydrate Active Enzymes (CAZymes). This research highlights how underlying dynamic features of proteins can be utilized for the design and mechanistic interpretation of biomolecular function in a broad range of applications.
dc.description.sponsorshipDustin D. Smith received an Alberta Innovates Graduate Student Scholarship and a University of Lethbridge School of Graduate Studies Tuition Scholarship for this work.
dc.identifier.citationChapter 2: Smith, D.D., Girodat, D., Abbott, D.W., and Wieden, H.-J. (2022) Construction of a highly specific and selective carbohydrate-detecting biosensor utilizing Computational Identification of Non-disruptive Conjugation sites (CINC) for flexible and streamlined biosensor design. Biosensors and Bioelectronics, 200, 113899.; Chapter 3: Smith, D.D., King, J.K., Abbott, D.W., and Wieden, H.-J. (2022). Development of a real-time pectic oligosaccharide-detecting biosensor using the rapid and flexible Computational Identification of Non-disruptive Conjugation sites (CINC) biosensor design platform. Sensors, 22(3), 948.
dc.identifier.urihttps://hdl.handle.net/10133/6515
dc.language.isoen
dc.proquest.subject0487
dc.proquest.subject0786
dc.proquest.subject0307
dc.proquestyesYes
dc.publisherLethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry
dc.publisher.departmentDepartment of Chemistry and Biochemistry
dc.publisher.facultyArts and Science
dc.relation.ispartofseriesThesis (University of Lethbridge. Faculty of Arts and Science)
dc.subjectBiosensor
dc.subjectMolecular Dynamics
dc.subjectFluorescence
dc.subjectProtein Engineering
dc.subjectCarbohydrate Detection
dc.subjectRapid Kinetics
dc.subjectProtein Dynamics
dc.subjectAmino Acid Dynamics
dc.subjectCAZyme
dc.subjectProtein-fluorophore conjugate
dc.subjectCarbohydrate Active Enzyme
dc.titleCharacterization and rational design of biomolecular sensors using molecular dynamics simulations
dc.typeThesis
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