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Poster
in
Workshop: Generative and Experimental Perspectives for Biomolecular Design

AI-accelerated biocatalyst engineering by rapid microfluidic sequence-function mapping

Maximilian Gantz · Simon Mathis · Friederike E.H. Nintzel · Paul Zurek · Tanja Knaus · Elie Patel · Daniel Boros · Friedrich-Maximilian Weberling · Elliot J. Medcalf · Jacob Moss · Michael Herger · Tomasz Kaminski · Francesco Mutti · Pietro Lio · Florian Hollfelder


Abstract: Engineering biocatalysts is central for sustainable chemical synthesis, but hampered by a lack of sequence-function data which is costly and slow to obtain. We introduce a new microfluidic workflow, droplet lrDMS, which allows us to screen tens of thousands of enzyme variants within two weeks, a scale, speed and cost not feasible with plate screening or robotic workflows. Using this workflow, we generate large-scale sequence-function data of an imine reductase and rationally engineer improved variants with an up to 11-fold improvement in catalytic efficiency ($k_\text{cat}/K_M$) vs wild type. With machine learning, we further enhance catalytic efficiency up to 16-fold vs wild type, 4-fold better than the best variant in the dataset, by combining rational engineering and predictions from the AI model. The improvement is driven by a 24-fold improvement of catalytic rate ($k_\text{cat}$) over wild type significantly higher than rate improvements observed in an AI-informed campaign with a similar enzyme. Our study demonstrates the potential of droplet lrDMS sequence-function data to accelerate directed evolution by AI-informed biocatalyst engineering.

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