Lynn Wong : PhD Proposal Defense

Integrating in silico protein engineering strategies to modulate ligand-binding protein properties for use in a multiplex metabolite profiler

Dr. Govind Rao

Ligand-binding proteins have numerous applications, one of them being biosensors. They generally have moderate binding affinity for various small molecules, usually in the millimolar to micromolar range. Many clinically relevant metabolites fall in the micromolar concentration range in tissues or blood; hence, naturally occurring ligand-binding proteins provide a good basis for further engineering efforts to modulate their binding affinities. These binding proteins can be used in the production of low-cost point-of-care diagnostics. However, one of the challenges in building such a device is the identification and engineering of ligand-binding proteins for generating a library of biosensors to detect various metabolites. This is further complicated by the lack of crystal structures for some proteins of interest, which poses an obstacle to generating mutants via rational design. In this study, we will develop a design-build-test platform to facilitate engineering mutant binding proteins by first implementing a set of assays of reasonable throughput, which in turn will determine the protein design strategy that can be applied. Also, we will explore computational protein design to model protein-ligand interactions and evaluate homology modeling to predict protein structures of closely related proteins by phylogeny. Finally, various microsampling methods will be studied to accommodate the utilization of these protein biosensors.