Computational Design and Directed Evolution of Novel Enzymes

Abstract

Enzymes are the most specific and active catalysts found in nature, and offer unique chemical properties suited to solving important industrial, medical, and environmental problems. In this work I present new methods for designing and evolving enzymes. In Chapter 1, I describe the theory and method of enzyme design, using the example of designing an enzyme for the Diels-Alder cycloaddition. In Chapter 2, I present the improvement of a computationally designed ester hydrolase enzyme through directed evolution and rational design. This work illustrates the insights that can be gained by performing directed evolution on computationally designed enzymes. In Chapter 3, I present the computational design and experimental characterization of novel alkyltransferase proteins. These proteins are particularly amenable to directed evolution, through which insight can be gained into possible improvements to future design efforts.