Opportunities and challenges for machine learning-assisted enzyme engineering

J Yang, FZ Li, FH Arnold - ACS Central Science, 2024 - ACS Publications
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …

Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Engineered enzymes for the synthesis of pharmaceuticals and other high-value products

MT Reetz, G Qu, Z Sun - Nature Synthesis, 2024 - nature.com
Catalysis has a central role in organic synthetic methodology, especially in stereoselective
reactions. In many reactions, enantioselectivity is made possible through the use of chiral …

Engineered cytochrome P450 for direct arylalkene-to-ketone oxidation via highly reactive carbocation intermediates

S Gergel, J Soler, A Klein, KH Schülke, B Hauer… - Nature Catalysis, 2023 - nature.com
Ketones are crucial intermediates in synthesis and frequent moieties in many products. The
direct regioselective synthesis of ketones from internal alkenes could simplify synthetic …

Flexibility regulation of loops surrounding the tunnel entrance in cytochrome P450 enhanced substrate access substantially

Z Li, S Meng, K Nie, U Schwaneberg, MD Davari… - ACS …, 2022 - ACS Publications
In recent years, the engineering of flexible loops to improve enzyme properties has gained
attention in biocatalysis. Herein, we report a loop engineering strategy to improve the …

Resha** substrate-binding pocket of leucine dehydrogenase for bidirectionally accessing structurally diverse substrates

T Wu, Y Wang, N Zhang, D Yin, Y Xu, Y Nie, X Mu - ACS Catalysis, 2022 - ACS Publications
Steric hindrance modification-based pocket resha** is an effective approach for enzyme–
substrate acceptance evolution. However, previous studies were limited to using the …

Learning from protein engineering by deconvolution of multi‐mutational variants

F Hollmann, J Sanchis, MT Reetz - … Chemie International Edition, 2024 - Wiley Online Library
This review analyzes a development in biochemistry, enzymology and biotechnology that
originally came as a surprise. Following the establishment of directed evolution of …

Choose your own adventure: A comprehensive database of reactions catalyzed by cytochrome P450 BM3 variants

DJ Fansher, JN Besna, A Fendri, JN Pelletier - ACS catalysis, 2024 - ACS Publications
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many
researchers have evolved this enzyme to generate a variety of products. However, the …

NMR-guided directed evolution

S Bhattacharya, EG Margheritis, K Takahashi… - Nature, 2022 - nature.com
Directed evolution is a powerful tool for improving existing properties and imparting
completely new functionalities to proteins,,–. Nonetheless, its potential in even small …

Counteraction of stability-activity trade-off of Nattokinase through flexible region shifting

J Luo, C Song, W Cui, L Han, Z Zhou - Food Chemistry, 2023 - Elsevier
The widespread trade-off between stability and activity severely limits enzyme evolution.
Although some progresses have been made to overcome this limitation, the counteraction …