UC Riverside

The objective of my Ph.D. study is to develop novel genetically encoded fluorescent biosensors to image and dissect biological signaling pathways in the context of live cells. I utilized protein engineering techniques to convert fluorescent proteins into fluorescent biosensors that can actively respond to specific, spatiotemporally organized cellular changes.

In this thesis, we expanded the fluorescent protein toolkit by engineering one of the first red fluorescent probes⎯rxRFP1⎯for sensing general redox states in the live cells. To further extend the usage of this sensor in various subcellular domains, such as mitochondria, endoplasmic reticulum, and the cell nucleus, we developed a group of rxRFP1 mutants showing different midpoint redox potentials for studying compartmentalized redox dynamics under various pathophysiological conditions. We also developed the first genetically encoded fluorescent biosensor for thioredoxin (Trx) redox by engineering a redox relay between the active-site cysteines of human Trx1 and rxRFP1. We utilized the resultant biosensor⎯TrxRFP1⎯to selectively monitor the perturbations of Trx redox in various mammalian cell lines. We further combined TrxRFP1 with a green fluorescent Grx1-roGFP2 biosensor to simultaneously monitor the dynamics of the two major cellular antioxidant systems, Trx and glutathione, in live cells in response to chemically and physiologically relevant stimuli.

We exploit another strategy which introduces reactive functional groups into circular permutated fluorescent proteins (cpFPs) using a genetic code expansion technology. Through a powerful directed protein evolution process, we were able to modulate the reactivity and chemoselectivity of an introduced p-boronophenylalanine (pBoF) in a cpRFP scaffold, resulting in fluorescent probes selectively responsive to hydrogen peroxide (H2O2) and peroxynitrite (ONOO—). Furthermore, by using boronic acid and short peptides as synergistic recognition motifs, we were able to engineer a series of reversible probes for nucleotides and carbohydrates showing surprisingly high specificity and large dynamic ranges. We have successfully utilized this new family of fluorescent probes to visualize various cellular activities.