Biocatalysis and Enzyme Design
We utilize multiscale computational modeling to study biocatalytic reaction mechanisms and selectivity-determining steps. We reveal the roles of beneficial mutations in engineered enzymes leading to enhanced catalyst performance. We leverage DFT-transition state calculations and classical MD simulations to facilitate de novo enzyme design for stereoselective biocatalytic reactions.
Research Interests
Our research aims to provide new mechanistic understanding of stereoselective biocatalytic reactions and to faciliate the experimental development of enzyme catalysts.
Mechanisms of stereoselective biocatalytic reactions
Due to their ability to exert exquisite stereocontrol over challenging chemical reactions, enzymes are excellent catalysts for asymmetric synthesis. Recent advancements in protein engineering allowed for efficient experimental development of new-to-nature reactions with repurposed enzymes, which promises to expand the reaction space of biocatalysis to activation modes unprecedented in biochemistry. However, understanding the mechanisms and origin of stereoselectivity in these enzymatic transformations is not trivial, because they often involve novel activation modes and elementary steps that are uncommon in organic chemistry, such as stereoselective radical addition/cyclization, long-range electron transfer, and proton-coupled electron transfer. In addition, studying the enzyme-controlled reactivity and selectivity requires considering the dynamic environment created by active site residues, which not only impacts the bond formation/cleavage transition states, but also substrate binding and transport processes. Our group implements a multiscaling modeling workflow that incorporates different computational techniques, including both quantum mechanics and molecular mechanics methods, to provide insights into the reaction mechanisms, stereoselectivity-determining steps, and how active site residues affect the reactivity and selectivity outcomes of the catalytic reactions.
Representative Publications:
-
Multiscale computational modeling revealed the enantioselectivity-determining step of the P411-catalyzed enantioselective C–H amination
-
JACS 2022, 144, 11215–11225. DOI: 10.1021/jacs.2c02283
-
-
The unexpected role of a glutamine residue (Q263) acting as the hydrogen bond donor to activate the substrate and enhance the enantioselectivity in radical cyclization
-
JACS 2022, 144, 13344–13355. DOI: 10.1021/jacs.2c04937
-
-
Catalytic mechanism of asymmetric radical cyclizatio catalyzed by engineered P450 enzymes
-
Science 2021, 374, 1612–1616. DOI: 10.1126/science.abk1603
-
-
Mechanism of a radical-mediated biocatalytic C–C coupling and the enzyme-controlled regioselectivity
-
Science 2023, 381, 444–451. DOI: 10.1126/science.adg2420
-
De novo enzyme design
Our group incorporates computational chemistry data, including DFT-computed transition state models and classical MD analysis of enzyme-substrate interactions, to faciliate the design of de novo enzymes for stereoselective reactions. Through collaborations with DeGrado (UCSF) and Yang (UCSB), we recently applied this workflow into the design of four-helix bundle enzymes for stereoselective carbene cyclopropanation, Si–H insertion, and Ge–H insertion.
Representative Publications:
-
De novo enzyme design for carbene cyclopropanation and Si–H insertion
-
Science 2025, 388, 665–670. DOI: 10.1126/science.adt7268
-
-
De novo enzyme design for carbene Ge–H insertion
-
JACS 2025, 147, 40869–40878. DOI: 10.1021/jacs.5c13909
-