Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

28 February 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of Protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.


Electrostatic Preorganization
Electric Fields
Enzyme catalysis
Directed Evolution
Enzyme Design

Supplementary materials

Supporting Information for Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field
Supporting Figures and Tables.


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