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 …

Evolving strategies for enzyme engineering

JD Bloom, MM Meyer, P Meinhold, CR Otey… - Current opinion in …, 2005 - Elsevier
Directed evolution is a common technique to engineer enzymes for a diverse set of
applications. Structural information and an understanding of how proteins respond to …

Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production

JC Greenhalgh, SA Fahlberg, BF Pfleger… - Nature …, 2021 - nature.com
Alcohol-forming fatty acyl reductases (FARs) catalyze the reduction of thioesters to alcohols
and are key enzymes for microbial production of fatty alcohols. Many metabolic engineering …

A family of thermostable fungal cellulases created by structure-guided recombination

P Heinzelman, CD Snow, I Wu… - Proceedings of the …, 2009 - National Acad Sciences
SCHEMA structure-guided recombination of 3 fungal class II cellobiohydrolases (CBH II
cellulases) has yielded a collection of highly thermostable CBH II chimeras. Twenty-three of …

Laboratory-directed protein evolution

L Yuan, I Kurek, J English… - … and Molecular Biology …, 2005 - Am Soc Microbiol
Systematic approaches to directed evolution of proteins have been documented since the
1970s. The ability to recruit new protein functions arises from the considerable substrate …

In vivo selection of a computationally designed SCHEMA AAV library yields a novel variant for infection of adult neural stem cells in the SVZ

DS Ojala, S Sun, JL Santiago-Ortiz, MG Shapiro… - Molecular Therapy, 2018 - cell.com
Directed evolution continues to expand the capabilities of complex biomolecules for a range
of applications, such as adeno-associated virus vectors for gene therapy; however …

Self-driving laboratories to autonomously navigate the protein fitness landscape

JT Rapp, BJ Bremer, PA Romero - Nature chemical engineering, 2024 - nature.com
Protein engineering has nearly limitless applications across chemistry, energy and
medicine, but creating new proteins with improved or novel functions remains slow, labor …

Next step in gene delivery: modern approaches and further perspectives of AAV tropism modification

MA Korneyenkov, AA Zamyatnin Jr - Pharmaceutics, 2021 - mdpi.com
Today, adeno-associated virus (AAV) is an extremely popular choice for gene therapy
delivery. The safety profile and simplicity of the genome organization are the decisive …

Structure-guided recombination creates an artificial family of cytochromes P450

CR Otey, M Landwehr, JB Endelman, K Hiraga… - PLoS …, 2006 - journals.plos.org
Creating artificial protein families affords new opportunities to explore the determinants of
structure and biological function free from many of the constraints of natural selection. We …

Optimal design of stochastic DNA synthesis protocols based on generative sequence models

EN Weinstein, AN Amin… - International …, 2022 - proceedings.mlr.press
Generative probabilistic models of biological sequences have widespread existing and
potential applications in analyzing, predicting and designing proteins, RNA and genomes …