Data-driven enzyme engineering to identify function-enhancing enzymes

Y Jiang, X Ran, ZJ Yang - Protein Engineering, Design and …, 2023 - academic.oup.com
Identifying function-enhancing enzyme variants is a 'holy grail'challenge in protein science
because it will allow researchers to expand the biocatalytic toolbox for late-stage …

Mutexa: a computational ecosystem for intelligent protein engineering

ZJ Yang, Q Shao, Y Jiang, C Jurich, X Ran… - Journal of Chemical …, 2023 - ACS Publications
Protein engineering holds immense promise in shaping the future of biomedicine and
biotechnology. This Review focuses on our ongoing development of Mutexa, a …

EnzyHTP computational directed evolution with adaptive resource allocation

Q Shao, Y Jiang, ZJ Yang - Journal of Chemical Information and …, 2023 - ACS Publications
Directed evolution facilitates enzyme engineering via iterative rounds of mutagenesis.
Despite the wide applications of high-throughput screening, building “smart libraries” to …

Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis

Y Jiang, N Ding, Q Shao, SL Stull… - The Journal of …, 2023 - ACS Publications
Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby
influencing catalytic efficiency. However, it remains unknown whether SPD effects originate …

[HTML][HTML] Endocrine-disrupting metabolic activation of 2-nitrofluorene catalyzed by human cytochrome P450 1A1: A QM/MM approach

J Zhou, X Zhang, Y Li, S Feng, Q Zhang… - Environment International, 2022 - Elsevier
Nitropolycyclic aromatic hydrocarbons (NPAHs) present one of the most important airborne
pollutants. Recent studies have shown that one of the most abundant NPAHs, 2 …

Origin of metabolites diversity and selectivity of P450 catalyzed benzo [a] pyrene metabolic activation

S Feng, Y Li, R Zhang, Q Zhang, W Wang - Journal of Hazardous Materials, 2022 - Elsevier
Abstract Polycyclic Aromatic Hydrocarbon (PAHs) presents one of the most abundant class
of environmental pollutants. Recent study shows a lab-synthesized PAHs derivative …

LassoHTP: a high-throughput computational tool for lasso peptide structure construction and modeling

RJ Juarez, Y Jiang, M Tremblay, Q Shao… - Journal of chemical …, 2023 - ACS Publications
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified
peptides with a slipknot conformation. With superior thermal stability, protease resistance …

A multifunctional flavoprotein monooxygenase HspB for hydroxylation and CC cleavage of 6-hydroxy-3-succinoyl-pyridine

X Ouyang, G Liu, L Guo, G Wu, P Xu… - Applied and …, 2024 - Am Soc Microbiol
Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation,
involved in the catabolism, detoxification, and biosynthesis of natural substrates and …

Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations

JTS Coimbra, PA Fernandes… - Journal of Chemical …, 2023 - ACS Publications
Due to the emergence of antibiotic resistance, the need to explore novel antibiotics and/or
novel strategies to counter antibiotic resistance is of utmost importance. In this work, we …

IntEnzyDB: an Integrated Structure–Kinetics Enzymology Database

B Yan, X Ran, A Gollu, Z Cheng, X Zhou… - Journal of chemical …, 2022 - ACS Publications
Data-driven modeling has emerged as a new paradigm for biocatalyst design and discovery.
Biocatalytic databases that integrate enzyme structure and function data are in urgent need …