Opportunities and challenges in design and optimization of protein function

D Listov, CA Goverde, BE Correia… - … Reviews Molecular Cell …, 2024 - nature.com
The field of protein design has made remarkable progress over the past decade. Historically,
the low reliability of purely structure-based design methods limited their application, but …

[HTML][HTML] Engineering enzyme access tunnels

P Kokkonen, D Bednar, G Pinto, Z Prokop… - Biotechnology …, 2019 - Elsevier
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological
and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic …

Mechanism-guided tunnel engineering to increase the efficiency of a flavin-dependent halogenase

K Prakinee, A Phintha, S Visitsatthawong, N Lawan… - Nature Catalysis, 2022 - nature.com
Although flavin-dependent halogenases (FDHs) are attractive for C–H bond activation, their
applications are limited due to low turnover and stability. We have previously shown that …

Enabling peroxygenase activity in cytochrome P450 monooxygenases by engineering hydrogen peroxide tunnels

P Zhao, F Kong, Y Jiang, X Qin, X Tian… - Journal of the American …, 2023 - ACS Publications
Given prominent physicochemical similarities between H2O2 and water, we report a new
strategy for promoting the peroxygenase activity of P450 enzymes by engineering their …

Evolution of dynamical networks enhances catalysis in a designer enzyme

HA Bunzel, JLR Anderson, D Hilvert, VL Arcus… - Nature Chemistry, 2021 - nature.com
Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as
shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical …

Hot spots-making directed evolution easier

H Yu, S Ma, Y Li, PA Dalby - Biotechnology Advances, 2022 - Elsevier
Directed evolution has emerged as a powerful strategy to engineer various properties of
proteins. Traditional methods to construct libraries such as error-prone PCR and DNA …

Computational design of enzymes for biotechnological applications

J Planas-Iglesias, SM Marques, GP Pinto, M Musil… - Biotechnology …, 2021 - Elsevier
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their
natural effectiveness has been fine-tuned as a result of millions of years of natural evolution …

ProteinTools: a toolkit to analyze protein structures

N Ferruz, S Schmidt, B Höcker - Nucleic acids research, 2021 - academic.oup.com
The experimental characterization and computational prediction of protein structures has
become increasingly rapid and precise. However, the analysis of protein structures often …

[HTML][HTML] Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration

SM Kim, SH Kang, BW Jeon, YH Kim - Bioresource Technology, 2024 - Elsevier
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase
(H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the …

Emerging Strategies for Modifying Cytochrome P450 Monooxygenases into Peroxizymes

S Fan, Z Cong - Accounts of Chemical Research, 2024 - ACS Publications
Conspectus Cytochrome P450 monooxygenase is a versatile oxidizing enzyme with great
potential in synthetic chemistry and biology. However, the dependence of its catalytic …