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 …

Exploring protein fitness landscapes by directed evolution

PA Romero, FH Arnold - Nature reviews Molecular cell biology, 2009 - nature.com
Directed evolution circumvents our profound ignorance of how a protein's sequence
encodes its function by using iterative rounds of random mutation and artificial selection to …

Machine learning-assisted directed protein evolution with combinatorial libraries

Z Wu, SBJ Kan, RD Lewis, BJ Wittmann… - Proceedings of the …, 2019 - pnas.org
To reduce experimental effort associated with directed protein evolution and to explore the
sequence space encoded by mutating multiple positions simultaneously, we incorporate …

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

CB Macdonald, D Nedrud, PR Grimes, D Trinidad… - Genome biology, 2023 - Springer
Insertions and deletions (indels) enable evolution and cause disease. Due to technical
challenges, indels are left out of most mutational scans, limiting our understanding of them in …

Protein stability promotes evolvability

JD Bloom, ST Labthavikul, CR Otey… - Proceedings of the …, 2006 - pnas.org
The biophysical properties that enable proteins to so readily evolve to perform diverse
biochemical tasks are largely unknown. Here, we show that a protein's capacity to evolve is …

Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions

MT Reetz - Angewandte Chemie International Edition, 2011 - Wiley Online Library
Asymmetric catalysis plays a key role in modern synthetic organic chemistry, with synthetic
catalysts and enzymes being the two available options. During the latter part of the last …

Addressing the numbers problem in directed evolution

MT Reetz, D Kahakeaw, R Lohmer - ChemBioChem, 2008 - Wiley Online Library
Our previous contribution to increasing the efficiency of directed evolution is iterative
saturation mutagenesis (ISM) as a systematic means of generating focused libraries for the …

Evolving artificial metalloenzymes via random mutagenesis

H Yang, AM Swartz, HJ Park, P Srivastava… - Nature …, 2018 - nature.com
Random mutagenesis has the potential to optimize the efficiency and selectivity of protein
catalysts without requiring detailed knowledge of protein structure; however, introducing …

Ultrahigh‐throughput FACS‐based screening for directed enzyme evolution

G Yang, SG Withers - ChemBioChem, 2009 - Wiley Online Library
Directed enzyme evolution has proven to be a powerful tool for improving a range of
properties of enzymes through consecutive rounds of diversification and selection. However …