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 …

A guide to designing photocontrol in proteins: methods, strategies and applications

AC Kneuttinger - Biological Chemistry, 2022 - degruyter.com
Light is essential for various biochemical processes in all domains of life. In its presence
certain proteins inside a cell are excited, which either stimulates or inhibits subsequent …

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 …

Determinants of trafficking, conduction, and disease within a K+ channel revealed through multiparametric deep mutational scanning

W Coyote-Maestas, D Nedrud, Y He, D Schmidt - Elife, 2022 - elifesciences.org
A long-standing goal in protein science and clinical genetics is to develop quantitative
models of sequence, structure, and function relationships to understand how mutations …

Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling

W Coyote-Maestas, D Nedrud, A Suma, Y He… - Nature …, 2021 - nature.com
Protein domains are the basic units of protein structure and function. Comparative analysis
of genomes and proteomes showed that domain recombination is a main driver of …

Enlightening allostery: designing switchable proteins by photoreceptor fusion

J Mathony, D Niopek - Advanced Biology, 2021 - Wiley Online Library
Optogenetics harnesses natural photoreceptors to non‐invasively control selected
processes in cells with previously unmet spatiotemporal precision. Linking the activity of a …

Creation of a point-of-care therapeutics sensor using protein engineering, electrochemical sensing and electronic integration

R Cai, C Ngwadom, R Saxena, J Soman… - Nature …, 2024 - nature.com
Point-of-care sensors, which are low-cost and user-friendly, play a crucial role in precision
medicine by providing quick results for individuals. Here, we transform the conventional …

A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

TYH Ho, A Shao, Z Lu, H Savilahti… - Nature …, 2021 - nature.com
Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use
remains limited because the already intricate split site identification problem is often …

Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins

J Mathony, S Aschenbrenner, P Becker… - Advanced …, 2023 - Wiley Online Library
Abstract Domain insertion engineering is a promising approach to recombine the functions
of evolutionarily unrelated proteins. Insertion of light‐switchable receptor domains into a …

Determinants of multiheme cytochrome extracellular electron transfer uncovered by systematic peptide insertion

IJ Campbell, JT Atkinson, MD Carpenter… - Biochemistry, 2022 - ACS Publications
The multiheme cytochrome MtrA enables microbial respiration by transferring electrons
across the outer membrane to extracellular electron acceptors. While structural studies have …