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 …

[HTML][HTML] Insertions and deletions in protein evolution and engineering

S Savino, T Desmet, J Franceus - Biotechnology Advances, 2022 - Elsevier
Protein evolution or engineering studies are traditionally focused on amino acid
substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion …

Computational scoring and experimental evaluation of enzymes generated by neural networks

SR Johnson, X Fu, S Viknander, C Goldin… - Nature …, 2024 - nature.com
In recent years, generative protein sequence models have been developed to sample novel
sequences. However, predicting whether generated proteins will fold and function remains …

Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella sakaiensis PETase and Variants with Improved Stability and …

Y Joho, V Vongsouthi, MA Spence, J Ton, C Gomez… - Biochemistry, 2022 - ACS Publications
The improved production, recycling, and removal of plastic waste, such as polyethylene
terephthalate (PET), are pressing environmental and economic issues for society …

Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors

MC Derbyshire, S Raffaele - Nature Communications, 2023 - nature.com
Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors
are engaged in a molecular arms race with the host resulting in conflicting evolutionary …

Insertions and deletions: Computational methods, evolutionary dynamics, and biological applications

BD Redelings, I Holmes, G Lunter… - Molecular biology …, 2024 - academic.oup.com
Insertions and deletions constitute the second most important source of natural genomic
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …

Evolution of phosphorylase activity in an ancestral glycosyltransferase

J Franceus, JP Rivas-Fernandez, J Lormans… - ACS …, 2024 - ACS Publications
The reconstruction of ancestral sequences can offer a glimpse into the fascinating process of
molecular evolution by exposing the adaptive pathways that shape the proteins found in …

Chromosome‐level genome assembly of Prunella vulgaris L. provides insights into pentacyclic triterpenoid biosynthesis

S Zhang, F Meng, X Pan, X Qiu, C Li, S Lu - The Plant Journal, 2024 - Wiley Online Library
Prunella vulgaris is one of the bestselling and widely used medicinal herbs. It is recorded as
an ace medicine for cleansing and protecting the liver in Chinese Pharmacopoeia and has …

Engineering Biocatalysts for the C− H Activation of Fatty Acids by Ancestral Sequence Reconstruction

BS Jones, CM Ross, G Foley… - Angewandte Chemie …, 2024 - Wiley Online Library
Selective, one‐step C− H activation of fatty acids from biomass is an attractive concept in
sustainable chemistry. Biocatalysis has shown promise for generating high‐value hydroxy …

Optimal phylogenetic reconstruction of insertion and deletion events

S Tule, G Foley, C Zhao, M Forbes, M Bodén - Bioinformatics, 2024 - academic.oup.com
Motivation Insertions and deletions (indels) influence the genetic code in fundamentally
distinct ways from substitutions, significantly impacting gene product structure and function …