Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 9, 2024

Abstract Successes in biocatalytic polyester recycling have raised the possibility of deconstructing alternative polymers enzymatically, with polyamide (PA) being a logical target due to array amide-cleaving enzymes present nature. Here, we screen 40 potential natural and engineered nylon-hydrolyzing (nylonases), using mass spectrometry quantify eight compounds resulting from enzymatic nylon-6 (PA6) hydrolysis. Comparative time-course reactions incubated at 40-70 °C showcase enzyme-dependent variations product distributions extent PA6 film depolymerization, significant nylon deconstruction activity appearing rare. The most active nylonase, NylC K variant rationally thermostabilized (an N-terminal nucleophile (Ntn) hydrolase, -TS, T m = 87.4 °C, 16.4 higher than wild-type), hydrolyzes 0.67 wt% film. Reactions fail restart after fresh enzyme addition, indicating that substrate-based limitations, such as restricted access hydrolysable bonds, prohibit more extensive deconstruction. Overall, this study expands our understanding nylonase distribution, indicates Ntn hydrolases may greatest for further development, identifies key targets progressing including improving activity, selectivity, enhancing polymer accessibility.

Language: Английский

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Engineering Enzymes for Environmental Sustainability

Angewandte Chemie International Edition, Journal Year: 2023, Volume and Issue: 62(52)

Published: Aug. 31, 2023

Abstract The development and implementation of sustainable catalytic technologies is key to delivering our net‐zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed improve the sustainability numerous processes help conserve environment. Efficient robust biocatalysts have been capture carbon dioxide (CO 2 ) embedded into new efficient metabolic CO fixation pathways. Enzymes refined for bioremediation, enhancing their ability degrade toxic harmful pollutants. Biocatalytic recycling gaining momentum, cutinases PETases depolymerization abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches accessing petroleum‐based feedstocks chemicals are expanding, optimized enzymes convert plant biomass biofuels or other high value products. Through these examples, hope illustrate enzyme engineering biocatalysis contribute cleaner more chemical industry.

Language: Английский

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Target-Navigated CBT–Cys “Stapling” Coupled with CRISPR/Cas12a Amplification for the Photoelectrochemical Nucleic Acid Assay

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(45), P. 18011 - 18019

Published: Sept. 27, 2024

Generally, rolling circle amplification (RCA) is based on an enzyme-linked padlock extension reaction. Herein, rapid linking that utilizes click chemistry for joining sticky ends of DNA molecules was developed. The nucleic acid were modified with 2-cyano-6-aminobenzothiazole (CBT) and cystine (Cys-Cys), while glutathione introduced to break the disulfide bond under target navigation promote linkage between CBT Cys at terminus pH 7.4. Subsequently, RCA performed using phi29 polymerase. CRISPR/Cas12a cleavage triggered by product amplification. Assisted alkaline phosphatase, electron exchange process photoelectroactive Sb@Co(OH)F nanorod

Language: Английский

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Strategies for designing biocatalysts with new functions

Chemical Society Reviews, Journal Year: 2024, Volume and Issue: 53(6), P. 2851 - 2862

Published: Jan. 1, 2024

Enzymes can be optimized to accelerate chemical transformations via a range of methods. In this review, we showcase how protein engineering and computational design techniques interfaced develop highly efficient selective biocatalysts.

Language: Английский

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Biocatalytic enzymes in food packaging, biomedical, and biotechnological applications: A comprehensive review

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 140069 - 140069

Published: Jan. 1, 2025

Language: Английский

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Deep-ProBind: binding protein prediction with transformer-based deep learning model

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 22, 2025

Binding proteins play a crucial role in biological systems by selectively interacting with specific molecules, such as DNA, RNA, or peptides, to regulate various cellular processes. Their ability recognize and bind target molecules high specificity makes them essential for signal transduction, transport, enzymatic activity. Traditional experimental methods identifying protein-binding peptides are costly time-consuming. Current sequence-based approaches often struggle accuracy, focusing too narrowly on proximal sequence features ignoring structural data. This study presents Deep-ProBind, powerful prediction model designed classify protein binding sites integrating information. The proposed employs transformer evolutionary-based attention mechanism, i.e., Bidirectional Encoder Representations from Transformers (BERT) Pseudo position scoring matrix -Discrete Wavelet Transform (PsePSSM -DWT) approach encode peptides. SHapley Additive exPlanations (SHAP) algorithm selects the optimal hybrid features, Deep Neural Network (DNN) is then used classification predict performance of was evaluated comparison traditional Machine Learning (ML) algorithms existing models. Experimental results demonstrate that Deep-ProBind achieved 92.67% accuracy tenfold cross-validation benchmark datasets 93.62% independent samples. outperforms models 3.57% training data 1.52% tests. These Deep-ProBind's reliability effectiveness, making it valuable tool researchers potential resource pharmacological studies, where peptide plays critical therapeutic development.

Language: Английский

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Enhancing enzymatic activity with nanoparticle display – an updated compendium and engineering outlook

Molecular Systems Design & Engineering, Journal Year: 2024, Volume and Issue: 9(7), P. 679 - 704

Published: Jan. 1, 2024

Schematic depicting enzyme kinetic enhancement when displayed on a nanoparticle surface. We provide state of the art review this phenomenon describing what is known about how it arises along with examples grouped by nanomaterials.

Language: Английский

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One-pot biocatalytic upgrading of lignin-derived phenol and catechol to hydroxytyrosol

Green Chemistry, Journal Year: 2024, Volume and Issue: 26(10), P. 6180 - 6189

Published: Jan. 1, 2024

One-pot cascade biocatalysis for the conversion of renewable lignin-derived phenol and catechol into hydroxytyrosol.

Language: Английский

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Use of Nicotinamide Mononucleotide as Non-Natural Cofactor

Catalysts, Journal Year: 2025, Volume and Issue: 15(1), P. 37 - 37

Published: Jan. 3, 2025

Nicotinamide mononucleotide (NMN) has emerged as a promising non-natural cofactor with significant potential to transform biocatalysis, synthetic biology, and therapeutic applications. By modulating NAD⁺ metabolism, NMN offers unique advantages in enzymatic reactions, metabolic engineering, regenerative medicine. This review provides comprehensive analysis of NMN’s biochemical properties, mechanisms action, diverse Emphasis is placed on its role addressing challenges multi-enzyme cascades, biofuel production, the synthesis high-value chemicals. The paper also highlights critical research gaps, including need for scalable methods, improved integration into systems, toxicity studies use. Emerging technologies such AI-driven enzyme design CRISPR-based genome engineering are discussed transformative tools optimizing NMN-dependent pathways. Furthermore, synergistic biology innovations, cell-free systems dynamic regulatory networks, explored, paving way precise modular biotechnological solutions. Looking forward, versatility positions it pivotal tool advancing sustainable bioprocessing precision Addressing current limitations through interdisciplinary approaches will enable redefine boundaries innovation. serves roadmap leveraging across scientific industrial domains.

Language: Английский

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Perspectives on the microorganisms with the potentials of PET-degradation

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: March 12, 2025

Polyethylene terephthalate (PET), a widely used synthetic polymer in daily life, has become major source of post-consumer waste due to its complex molecular structure and resistance natural degradation, which posed significant threat the global ecological environment human health. Current PET-processing methods include physical, chemical, biological approaches, however each have their limitations. Given that numerous microbial strains exhibit remarkable capacity degrade plastic materials, degradation PET emerged as highly promising alternative. This approach not only offers possibility converting into valuable resources but also contributes advancement circular economy. Therefore this review, it is mainly focused on cutting-edge technologies key role specific such Ideonella sakaiensis 201-F6, can efficiently assimilate PET. Particularly noteworthy are catalytic enzymes related metabolism PET, been emphasized sustainable eco-friendly strategy for recycling within framework Furthermore, study elucidates innovative utilization degraded materials feedstock production high-value chemicals, highlighting path forward management waste.

Language: Английский

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