Synthetic biology: bottom-up assembly of molecular systems

S Hirschi, TR Ward, WP Meier, DJ Müller… - Chemical …, 2022 - ACS Publications
The bottom-up assembly of biological and chemical components opens exciting
opportunities to engineer artificial vesicular systems for applications with previously unmet …

Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

M Gantz, S Neun, EJ Medcalf, LD van Vliet… - Chemical …, 2023 - ACS Publications
Novel and improved biocatalysts are increasingly sourced from libraries via experimental
screening. The success of such campaigns is crucially dependent on the number of …

[HTML][HTML] 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 …

[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 …

[HTML][HTML] Engineering the protein dynamics of an ancestral luciferase

A Schenkmayerova, GP Pinto, M Toul, M Marek… - Nature …, 2021 - nature.com
Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has
proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable …

[HTML][HTML] A primer to directed evolution: current methodologies and future directions

LS Vidal, M Isalan, JT Heap… - RSC Chemical Biology, 2023 - pubs.rsc.org
Directed evolution is one of the most powerful tools for protein engineering and functions by
harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of …

Mechanisms of protein evolution

V Jayaraman, S Toledo‐Patiño, L Noda‐García… - Protein …, 2022 - Wiley Online Library
How do proteins evolve? How do changes in sequence mediate changes in protein
structure, and in turn in function? This question has multiple angles, ranging from …

Insertions and deletions (indels): a missing piece of the protein engineering jigsaw

CM Miton, N Tokuriki - Biochemistry, 2022 - ACS Publications
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate
protein evolution in the test tube. While there have been considerable advances, our ability …

[HTML][HTML] An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation

M Seuma, B Lehner, B Bolognesi - Nature Communications, 2022 - nature.com
Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal
disease mechanisms. To date, MAVEs have focussed on a single mutation type—amino …

A mechanistic view of enzyme evolution

G Yang, CM Miton, N Tokuriki - Protein Science, 2020 - Wiley Online Library
New enzyme functions often evolve through the recruitment and optimization of latent
promiscuous activities. How do mutations alter the molecular architecture of enzymes to …