S114: Integrating enzyme design and metabolic engineering to ferment high value chemicals

The recent emergence of industrial and synthetic biotechnology has the potential to radically transform the chemical industry. Despite significant success, the availability of efficient biocatalysts is one of the major limitations to design novel cell factories that can produce valuable chemicals renewably. To this end, we developed novel computational methods and applied them to rationally engineer enzymes with a wide range of activities, including the de novo design of enzymes catalyzing a retro-aldol reaction, a Kemp elimination reaction, and a Diels-Alder reaction. To complement our previous techniques, we have recently developed a new algorithm, called Enzyme Identification™, to rapidly engineer enzymes with known catalytic mechanisms for non-native substrates. For a given chemical reaction, our algorithm screens “in silico” large databases of structural and sequence information to allow the rapid discovery of existing enzymes that possess both the necessary catalytic machinery and an appropriate substrate binding pocket. For those enzymes that possess the necessary catalytic machinery but lack an active site that can accommodate the substrate(s) of interest, Enzyme Identification automatically redesigns and remodels the active site pocket thus enabling catalysis of the desired reaction. The demonstrated success and wide applicability of our methods open the way for the design of a variety of novel biocatalyst necessary for the efficient development of biosynthetic pathways for the industrial scale fermentation of high value chemicals.