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 …

Artificial metalloenzymes

T Vornholt, F Leiss-Maier, WJ Jeong… - Nature Reviews …, 2024 - nature.com
The development of artificial metalloenzymes (ArMs) aims to expand the capabilities of
enzymatic catalysis, most notably towards new reaction mechanisms. Frequently, ArMs …

Self-play reinforcement learning guides protein engineering

Y Wang, H Tang, L Huang, L Pan, L Yang… - Nature Machine …, 2023 - nature.com
Designing protein sequences towards desired properties is a fundamental goal of protein
engineering, with applications in drug discovery and enzymatic engineering. Machine …

A combinatorially complete epistatic fitness landscape in an enzyme active site

KE Johnston, PJ Almhjell, EJ Watkins-Dulaney… - Proceedings of the …, 2024 - pnas.org
Protein engineering often targets binding pockets or active sites which are enriched in
epistasis—nonadditive interactions between amino acid substitutions—and where the …

Emerging technologies for biocatalysis in the pharmaceutical industry

RD Lewis, SP France, CA Martinez - ACS Catalysis, 2023 - ACS Publications
Biocatalysis is a key technology in the pharmaceutical industry as it can provide efficient and
sustainable catalytic routes toward active pharmaceutical ingredients (APIs). The …

Learning epistasis and residue coevolution patterns: Current trends and future perspectives for advancing enzyme engineering

M Wittmund, F Cadet, MD Davari - ACS catalysis, 2022 - ACS Publications
Engineering proteins and enzymes with the desired functionality has broad applications in
molecular biology, biotechnology, biomedical sciences, health, and medicine. The vastness …

Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET

P Dutka, LA Metskas, RC Hurt, H Salahshoor, TY Wang… - Structure, 2023 - cell.com
Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of
bacteria and archaea as flotation devices to enable access to optimal light and nutrients …

Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning

T Vornholt, M Mutný, GW Schmidt… - ACS Central …, 2024 - ACS Publications
Tailored enzymes are crucial for the transition to a sustainable bioeconomy. However,
enzyme engineering is laborious and failure-prone due to its reliance on serendipity. The …

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Y Long, A Mora, FZ Li, E Gürsoy… - ACS Synthetic …, 2024 - ACS Publications
Sequence-function data provides valuable information about the protein functional
landscape but is rarely obtained during directed evolution campaigns. Here, we present …

Metabolic and cellular engineering for the production of natural products

D Yang, H Eun, CPS Prabowo, S Cho… - Current Opinion in …, 2022 - Elsevier
Highlights•Systems metabolic engineering has enabled efficient production of natural
products.•Systems-level engineering of metabolism has increased pathway efficiencies.•Cell …