FAIR Data and Software: Improving Efficiency and Quality of Biocatalytic Science DOI
Jürgen Pleiss

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(4), P. 2709 - 2718

Published: Feb. 7, 2024

Biocatalysis is entering a promising era as data-driven science. High-throughput experimentation generates rapidly increasing stream of biocatalytic data, which the raw material for mechanistic and modeling to design improved biocatalysts bioprocesses. However, our laboratory routines scientific practice communicating results are insufficient ensure reproducibility scalability experiments, data management has become bottleneck progress in biocatalysis. In order take full advantage rapid experimental computational technologies, should be findable, accessible, interoperable, reusable (FAIR). FAIRification software achieved by developing standardized exchange formats ontologies, electronic lab notebooks acquisition documentation experimentation, collaborative platforms analyzing repositories publishing together with data. The EnzymeML platform provides extensible tools FAIR scalable digitalization biocatalysis expected improve efficiency research automation guarantee quality science reproducibility. Most all, they foster reasoning creating hypotheses enabling reanalysis previously published thus promote disruptive innovation.

Language: Английский

Practical Machine Learning-Assisted Design Protocol for Protein Engineering: Transaminase Engineering for the Conversion of Bulky Substrates DOI
Marian J. Menke, Yu‐Fei Ao, Uwe T. Bornscheuer

et al.

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(9), P. 6462 - 6469

Published: April 12, 2024

Protein engineering is essential for improving the catalytic performance of enzymes applications in biocatalysis, which machine learning provides an emerging approach variant design. Transaminases are powerful biocatalysts stereoselective synthesis chiral amines but one major challenge their limited substrate scope. We present a general and practical design protocol protein to combine advantages three strategies, including directed evolution, rational design, learning, demonstrate application transaminases with higher activity toward bulky substrates. A high-quality data set was obtained by selected key positions, then applied create model transaminase activity. This data-assisted optimized variants, showed improved (up 3-fold over parent) substrates, maintaining enantioselectivity starting enzyme scaffold as well enantiomeric excess >99%ee).

Language: Английский

Citations

13
Controlled enzymatic synthesis of oligonucleotides DOI Creative Commons
Maëva Pichon, Marcel Hollenstein

Communications Chemistry, Journal Year: 2024, Volume and Issue: 7(1)

Published: June 18, 2024

Abstract Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not efficient that read sequencing) DNA/RNA. Alternative, biocatalytic methods de novo synthesis natural modified dire need circumvent limitations traditional synthetic approaches. This Perspective article summarizes recent progress made controlled enzymatic synthesis, where temporary blocked nucleotides incorporated into immobilized primers by polymerases. While robust protocols have been established DNA, RNA XNA more challenging. Nevertheless, using a suitable combination protected and polymerase has shown promises produce even though production long DNA/RNA/XNA sequences (>1000 nt) remains We surmise merging ligase- polymerase-based would help current shortcomings synthesis.

Language: Английский

Citations

12
Enzymes in “Green” Synthetic Chemistry: Laccase and Lipase DOI Creative Commons

Dieter M. Scheibel,

Ioan Pavel Ivanov Gitsov, Ivan Gitsov

et al.

Molecules, Journal Year: 2024, Volume and Issue: 29(5), P. 989 - 989

Published: Feb. 24, 2024

Enzymes play an important role in numerous natural processes and are increasingly being utilized as environmentally friendly substitutes alternatives to many common catalysts. Their essential advantages high catalytic efficiency, substrate specificity, minimal formation of byproducts, low energy demand. All these benefits make enzymes highly desirable targets academic research industrial development. This review has the modest aim briefly overviewing classification, mechanism action, basic kinetics reaction condition effects that across all six enzyme classes. Special attention is devoted immobilization strategies main tools improve resistance environmental stress factors (temperature, pH solvents) prolong lifecycle biocatalysts. The drawbacks methods such macromolecular crosslinking, solid scaffold carriers, entrapment, surface modification (covalent physical) discussed illustrated using examples. Among hundreds possibly thousands known recently discovered enzymes, hydrolases oxidoreductases distinguished by their relative availability, stability, wide use synthetic applications, which include pharmaceutics, food beverage treatments, clean-up, polymerizations. Two representatives those groups-laccase (an oxidoreductase) lipase (a hydrolase)-are at length, including structure, mechanism, diverse usage. Objective representation current status emerging trends provided conclusions.

Language: Английский

Citations

11
Immobilized Multi‐Enzyme/Nanozyme Biomimetic Cascade Catalysis for Biosensing Applications DOI
Xiaoli Cai,

Yuteng Huang,

Chengzhou Zhu

et al.

Advanced Healthcare Materials, Journal Year: 2024, Volume and Issue: unknown

Published: June 18, 2024

Multiple enzyme-induced cascade catalysis has an indispensable role in the process of complex life activities, and is widely used to construct robust biosensors for analyzing various targets. The immobilized multi-enzyme system a novel biomimetic strategy that immobilizes enzymes with different functions stable carriers simulate synergistic multiple biological systems, which enables high stability efficiency enzymatic catalysis. Nanozymes, type nanomaterial intrinsic enzyme-like characteristics excellent stabilities, are also applied instead achieving better catalytic performance reaction stability. Due good stability, reusability, remarkably efficiency, multi-enzyme/nanozyme systems show distinct advantages promoting signal transduction amplification, thereby attracting vast research interest biosensing applications. This review focuses on progress recent years. construction approaches, factors affecting applications sensitive discussed detail. Further, their challenges outlooks future study provided.

Language: Английский

Citations

11
Ground-state flavin-dependent enzymes catalyzed enantioselective radical trifluoromethylation DOI Creative Commons

Xinyu Duan,

Dong Cui,

Mengdi Wang

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 31, 2025

Language: Английский

Citations

1
Extensive gene mining and facile engineering of a novel carbonyl reductase for asymmetric synthesis of anti-aging (S)-Pro-Xylane from d-xylose DOI
Zhe Dou,

Penghui Hu,

Linlin Song

et al.

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 140976 - 140976

Published: Feb. 1, 2025

Language: Английский

Citations

1
Catalysis Enhanced by Catalyst Wettability DOI
Hui Yu, Liang Wang, Feng‐Shou Xiao

et al.

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

Heterogeneous catalysis is a surface phenomenon where the adsorption, desorption, and transfer of reactants products are critical for catalytic performance. Recent results show that catalyst wettability strongly related to products. In this review, we briefly summarize strategies regulating enrich reactants, accelerate desorption products, promote mass in heterogeneous catalysis. addition, explore insights into enhancement Finally, concerns challenges subject outlined, practical proposed regulation wettability. We hope review will be helpful designing highly efficient catalysts future.

Language: Английский

Citations

1
Multi-functional covalent polymer eutectogels based on deep eutectic solvents potential for sealable adhesive DOI
Yi Hu,

Jiamian Zhan,

Chunyi Pu

et al.

Chemical Engineering Journal, Journal Year: 2025, Volume and Issue: unknown, P. 161269 - 161269

Published: March 1, 2025

Language: Английский

Citations

1
Rational engineering of a thermostable α-oxoamine synthase biocatalyst expands the substrate scope and synthetic applicability DOI Creative Commons
Ben Ashley, Sam Mathew,

Mariyah Sajjad

et al.

Communications Chemistry, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 13, 2025

Abstract Carbon-carbon bond formation is one of the key pillars organic synthesis. Green, selective and efficient biocatalytic methods for such are therefore highly desirable. The α-oxoamine synthases (AOSs) a class pyridoxal 5’-phosphate (PLP)-dependent, irreversible, carbon-carbon bond-forming enzymes, which have been limited previously by their narrow substrate specificity requirement acyl-CoA thioester substrates. We recently characterized thermophilic enzyme from Thermus thermophilus ( Th AOS) with much broader scope described its use in chemo-biocatalytic cascade process to generate pyrroles good yields timescales. Herein, we report structure-guided engineering AOS arrive at variants able greatly expanded range amino acid simplified N-acetylcysteamine (SNAc) acyl-thioester crystal structure improved V79A variant bound PLP: l -penicillamine external aldimine ligand, provides insight into properties engineered biocatalyst.

Language: Английский

Citations

1
Data‐Driven Protein Engineering for Improving Catalytic Activity and Selectivity DOI Creative Commons
Yu‐Fei Ao,

Mark Dörr,

Marian J. Menke

et al.

ChemBioChem, Journal Year: 2023, Volume and Issue: 25(3)

Published: Nov. 29, 2023

Abstract Protein engineering is essential for altering the substrate scope, catalytic activity and selectivity of enzymes applications in biocatalysis. However, traditional approaches, such as directed evolution rational design, encounter challenge dealing with experimental screening process a large protein mutation space. Machine learning methods allow approximation fitness landscapes identification patterns using limited data, thus providing new avenue to guide campaigns. In this concept article, we review machine models that have been developed assess enzyme‐substrate‐catalysis performance relationships aiming improve through data‐driven engineering. Furthermore, prospect future development field provide additional strategies tools achieving desired activities selectivities.

Language: Английский

Citations

22