Research in the Taylor lab involves taking a multi-disciplinary approach to investigate problems at the biological chemistry interface. We strive to find ways to exploit enzymes found in nature to perform chemistry that can help advance the fields of chemistry and medicine, while also employing chemical synthesis to help answer questions of both biological and medical interest. In my lab, we perform enzyme mechanism determination, gene function assignment, enzyme inhibitor design, kinetic profiling of enzymes, computational biochemistry, biophysical characterization and small scale synthetic organic chemistry. These strategies are integratively combined toward achieving the following long-term goals:
(1) Developing bacterial enzyme inhibitors and other small molecules with medicinal applications,
(2) Engineering of microorganisms to improve the efficiency of biomass to biofuel conversion.
These investigations examine enzymes within the context of their superfamilies, incorporating computational methods to guide chemical biology experimentation. We have identified in these systems conserved amino acid residues and spatial patterns necessary for catalyzing a given reaction, for controlling substrate specificity and for promoting protein dynamic motions. Our ongoing studies will continue to use these strategies to examine how allostery and dynamics influence protein catalysis. These analyses are intended to allow for improvement in the world’s ability to predict function for uncharacterized enzymes and ultimately could lead to the de novo design and synthesis of efficient enzymes for the catalysis of non-natural reactions.
Goal 1: Medically Applied Research
A primary focus is exploring the contribution to pathogenesis of the bacterial cell surface components with the hope that understanding their biosynthesis and molecular function will allow for the development of small molecules with antimicrobial applications. Specifically, the lipopolysaccharide (LPS) biosynthetic enzymes of Gram-negative bacteria (which include the causes of common food-borne illnesses like Escherichia coli, Salmonella and Vibrio cholerae, amongst others) are being investigated due to their potential as drug targets. The heptosyltransferase enzymes were selected in part because their genetic disruption yields bacteria with attenuated virulence, altered biofilm forming ability, greater membrane permeability, and enhanced susceptibility to macrophages and antimicrobials. Also, since these related glycosyltransferase enzymes (Heptosyltransferases I, II and III) catalyze a series of consecutive heptose addition reactions with varying chemistry of bond formation, this system allows us to explore how enzymes control both the stereo- and regio-chemistry of these reactions. Investigation of the mechanism, kinetics and protein dynamics of these enzymatic reactions is ongoing. Development of enzyme inhibitors using computational biochemistry and high-throughput screening efforts for these and other nucleoside utilizing enzymes is under investigation. Furthermore, we are exploring the utility of sugars and glycolipids for modulating both cell-cell and protein-small molecule interactions.
Goal 2: Biofuel Production Research
Increased interest in biomass conversion to biofuels has led to critical evaluation of the environmental impact of non-fossil fuel carbon sources, which in turn has revealed surprising problems associated with biofuel development efforts of major biomass sources (i.e. corn, sugarcane, soy). In order to help improve efficiency and to reduce the environmental impact of biofuel production, our lab is working to develop non-sugar and non-food based compounds as carbon sources for biofuel production. One potential carbon source being investigated is lignin, which is produced as a waste product of the timberland, agricultural and biofuel industries, and makes up approximately 25 % of all non-fossil organic carbon on the planet. The metabolic pathways for the degradation of lignin are being investigated, and the enzymes of these pathways are being structurally, computationally and kinetically characterized. These enzymes will be mutated and engineered, to allow for development of an abbreviated metabolic pathway that could have future industrial applications.