Characterization and rational design of biomolecular sensors using molecular dynamics simulations

Biosensors 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.

Grantor dc:publisher

Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry

Year dc:date.issued

2023

Authors dc:creator

• Smith, Dustin D.
• University of Lethbridge. Faculty of Arts and Science

Advisors dc:contributor.supervisor

• Wieden, Hans-Joachim
• Patel, Trushar R.

• Biosensor
• Molecular Dynamics
• Fluorescence
• Protein Engineering
• Carbohydrate Detection
• Rapid Kinetics
• Protein Dynamics
• Amino Acid Dynamics
• CAZyme
• Protein-fluorophore conjugate
• Carbohydrate Active Enzyme

Language dc:language.iso

en

Identifier

hdl:10133/6515

OAI record oai:identifier

https://opus.uleth.ca/server/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Aopus.uleth.ca%3A10133%2F6515