Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Gabriel Foley, Ariane Mora, Connie M. Ross, Scott Bottoms, Leander Sützl, Marnie L. Lamprecht, Julian Zaugg, Alexandra Essebier, Brad Balderson, Rhys Newell, Raine E. S. Thomson, Bostjan Kobe, Ross T. Barnard, Luke Guddat, Gerhard Schenk, Jörg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth M. J. Gillam, Mikael Bodén and Arne Elofsson

PLoS Comput Biol, 2022, 18, e1010633
DOI: 10.1371/journal.pcbi.1010633

Overcoming the Challenges of Enzyme Evolution To Adapt Phosphotriesterase for V-Agent Decontamination

Andrew N. Bigley, Emily Desormeaux, Dao Feng Xiang, Sue Y. Bae, Steven P. Harvey and Frank M. Raushel

Biochemistry, 2019, 58, 2039
DOI: 10.1021/acs.biochem.9b00097

Predicting Antiviral Resistance Mutations in SARS-CoV-2 Main Protease with Computational and Experimental Screening

Vishnu M. Sasi, Sven Ullrich, Jennifer Ton, Sarah E. Fry, Jason Johansen-Leete, Richard J. Payne, Christoph Nitsche and Colin J. Jackson

Biochemistry, 2022, 61, 2495
DOI: 10.1021/acs.biochem.2c00489

Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset

Charlotte M. Miton, Stefanie Jonas, Gerhard Fischer, Fernanda Duarte, Mark F. Mohamed, Bert van Loo, Bálint Kintses, Shina C. L. Kamerlin, Nobuhiko Tokuriki, Marko Hyvönen and Florian Hollfelder

Proc. Natl. Acad. Sci. U.S.A., 2018, 115
DOI: 10.1073/pnas.1607817115

Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks

Janine N. Copp, Eyal Akiva, Patricia C. Babbitt and Nobuhiko Tokuriki

Biochemistry, 2018, 57, 4651
DOI: 10.1021/acs.biochem.8b00473

Substrate Analogues for the Enzyme-Catalyzed Detoxification of the Organophosphate Nerve Agents—Sarin, Soman, and Cyclosarin

Andrew N. Bigley, Steven P. Harvey, Tamari Narindoshvili and Frank M. Raushel

Biochemistry, 2021, 60, 2875
DOI: 10.1021/acs.biochem.1c00361

Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments

Alexander C. Carpenter, Adam M. Feist, Fergus S.M. Harrison, Ian T. Paulsen and Thomas C. Williams

Metabolic Engineering Communications, 2023, 17, e00227
DOI: 10.1016/j.mec.2023.e00227

Characterization and catalytic mechanism of a direct demethylsulfide hydrolase for catabolism of the methylthiol-s-triazine prometryn

Jun Tang, Jinjin Yao, Dandan Pan, Junwei Huang, Jie Wang, Qing X. Li, Fengshou Dong and Xiangwei Wu

Journal of Hazardous Materials, 2023, 446, 130708
DOI: 10.1016/j.jhazmat.2022.130708

Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains

Mahakaran Sandhu, John Z. Chen, Dana S. Matthews, Matthew A. Spence, Sacha B. Pulsford, Barnabas Gall, Joe A. Kaczmarski, James Nichols, Nobuhiko Tokuriki and Colin J. Jackson

Biochemistry, 2025, 64, 1673
DOI: 10.1021/acs.biochem.4c00673