Fedor Lab Personnel

I am studying the catalytic mechanism of the glmS ribozyme, which is also a riboswitch that provides negative feed back regulation of glmS gene expression. Previously we have used the fluorescence properties of a guanine analogue to determine the microscopic pKa of an essential guanine residue in the active site and have concluded that it participates in catalysis in its neutral protonated form. We are currently focusing on the role of the cofactor in the catalytic mechanism by acquiring pre-steady state kinetics of glmS cleavage promoted by several ligands that differ in intrinsic Brønsted base strength and binding affinity. We hope to be able to correlate cofactor promoted rates with cofactor base strength and binding affinity, as well as to determine the extent of proton transfer in the transition state. The results of these experiments will allow us to deduce the cofactor’s role in general acid base catalysis of glmS ribozyme cleavage.

	Martha J. Fedor, Ph.D. Principal Investigator mfedor@scripps.edu Fedor CV	Research in our laboratory focuses on RNA folding and catalysis with special interest in regulatory RNAs known as riboswitches. These RNA elements regulate bacterial gene expression in response to binding small ligands. We recently uncovered the first evidence of a new paradigm for RNA-mediated gene regulation when we found that the glmS riboswitch binds to an array of stimulatory and inhibitory glucose metabolites and integrates information about the overall metabolic state of the cell to control expression of the glmS gene. The glmS riboswitch response to multiple metabolites likely represents an early indication of a vast RNA-metabolite interactome that remains to be explored. The glmS riboswitch is also a ribozyme that mediates a self-cleavage reaction in which glucosamine-6-phosphate, its cognate metabolite, serves as a catalytic cofactor. We developed a novel method for determining nucleobase purine ionization states in the context of the fully functional riboswitch active site that helped us gain insight into role of the glucosamine-6-phosphate cofactor. Application of this method has allowed us to achieve a deeper understanding of the strategies used by all RNA enzymes to accomplish catalysis of biological reactions.
	Julia Viladoms Claverol, Ph.D. Research Associate viladoms@scripps.edu	I am studying the catalytic mechanism of the glmS ribozyme, which is also a riboswitch that provides negative feed back regulation of glmS gene expression. Previously we have used the fluorescence properties of a guanine analogue to determine the microscopic pKa of an essential guanine residue in the active site and have concluded that it participates in catalysis in its neutral protonated form. We are currently focusing on the role of the cofactor in the catalytic mechanism by acquiring pre-steady state kinetics of glmS cleavage promoted by several ligands that differ in intrinsic Brønsted base strength and binding affinity. We hope to be able to correlate cofactor promoted rates with cofactor base strength and binding affinity, as well as to determine the extent of proton transfer in the transition state. The results of these experiments will allow us to deduce the cofactor’s role in general acid base catalysis of glmS ribozyme cleavage.
	Peter Watson Graduate Student watsonp@scripps.edu	I am investigating riboswitch activity in vivo, in order to gain insight into riboswitch function amidst the complex milieu of intracellular metabolites. We recently discovered that the glmS riboswitch integrates information from inhibitory, as well as activating metabolite ligands. I am interested in extending these findings to gain a quantitative understanding of signal integration by riboswitches in vivo.
	Courtney Curtis Administrative Assistant CCurtis@scripps.edu	I provide administrative support for Dr. Fedor and laboratory personnel.