Research Summary
Enzyme design and evolution, AI/ML, biocatalysis, protein engineering, synthetic biology
Profile
Dual Affiliation with Division of Biology and Biological Engineering
Assistant: Cheryl Nakashima
My laboratory pioneered methods to direct the evolution of enzymes, and we continue to refine and develop new approaches to protein engineering. Our most recent efforts combine directed evolution, simulation, and machine learning to optimize enzymes and create new ones. We have applied our techniques to an array of important problems in biocatalysis, from pharmaceutical synthesis to biofuels to sensors and diagnostics. We have also made key contributions to the understanding of enzyme evolution in nature. Our work has been recognized by numerous awards, including the 2018 Nobel Prize in Chemistry.
2019-20
ChE/BE 163. Introduction to Biomolecular Engineering.
12 units (3-0-9); first term, 2019-20.
Prerequisites: Bi 8, Bi/Ch 110 or instructor's permission and CS 1 or equivalent.
The course introduces rational design and evolutionary methods for engineering functional protein and nucleic acid systems. Rational design topics include molecular modeling, positive and negative design paradigms, simulation and optimization of equilibrium and kinetic properties, design of catalysts, sensors, motors, and circuits. Evolutionary design topics include evolutionary mechanisms and tradeoffs, fitness landscapes, directed evolution of proteins, and metabolic pathways. Some assignments require programming (Python is the language of instruction).
Instructors: Arnold, Pierce
Instructors: Arnold, Pierce