Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Learning from protein engineering by deconvolution of multi‐mutational variants

F Hollmann, J Sanchis, MT Reetz - … Chemie International Edition, 2024 - Wiley Online Library
This review analyzes a development in biochemistry, enzymology and biotechnology that
originally came as a surprise. Following the establishment of directed evolution of …

Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

JJ Ruiz-Pernía, K Swiderek, J Bertran… - Journal of Chemical …, 2024 - ACS Publications
Enzyme design faces challenges related to the implementation of the basic principles that
govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic …

Advances in alginate lyases and the potential application of enzymatic prepared alginate oligosaccharides: A mini review

C Chen, X Li, C Lu, X Zhou, L Chen, C Qiu, Z **… - International Journal of …, 2024 - Elsevier
Alginate is mainly a linear polysaccharide composed of randomly arranged β-D-mannuronic
acid and α-L-guluronic acid linked by α, β-(1, 4)-glycosidic bonds. Alginate lyases degrade …

[HTML][HTML] Protein representations: Encoding biological information for machine learning in biocatalysis

D Harding-Larsen, J Funk, NG Madsen… - Biotechnology …, 2024 - Elsevier
Enzymes offer a more environmentally friendly and low-impact solution to conventional
chemistry, but they often require additional engineering for their application in industrial …

[HTML][HTML] Enzyme engineering for biocatalysis

C Paul, U Hanefeld, F Hollmann, G Qu, B Yuan… - Molecular Catalysis, 2024 - Elsevier
Contemporary Biocatalysis heavily relies on enzyme engineering as natural enzymes
frequently lack the requisite attributes for effective organic synthesis. The inherent limitations …

Combining flexible region design and automatic design to enhance the thermal stability and catalytic efficiency of leucine dehydrogenase

X Zhang, X Zhang, H Shi, H Zhang… - Journal of Agricultural …, 2024 - ACS Publications
Leucine dehydrogenase (LeuDH, EC 1.4. 1.9) can reversibly catalyze the oxidative
deamination of l-leucine and some other specific α-amino acids to form the corresponding α …

Comprehensive Understanding of Laboratory Evolution for Food Enzymes: From Design to Screening Innovations

J Wu, Z Wang, M Zeng, Z He, Q Chen… - Journal of Agricultural …, 2024 - ACS Publications
In the field of food processing, enzymes play a pivotal role in improving product quality and
flavor, and extending shelf life. However, the exposure of traditional food enzymes to high …

Water-mediated active conformational transitions of lipase on organic solvent interfaces

J Zhang, J Chen, Y Sha, J Deng, J Wu, P Yang… - International Journal of …, 2024 - Elsevier
When it comes to enzyme stability and their application in organic solvents, enzyme
biocatalysis has emerged as a popular substitute for conventional chemical processes …

Hook loop dynamics engineering transcended the barrier of activity-stability trade-off and boosted the thermostability of enzymes

W Chong, Z Zhang, Z Li, S Meng, B Nian… - International Journal of …, 2024 - Elsevier
The improvement of enzyme thermostability often accompanies the decreased activity due to
the loss of the key regions' flexibility. As a representative structure, unlocking the potential of …