1
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Pecchini P, Fochi M, Bartoccini F, Piersanti G, Bernardi L. Enantioselective organocatalytic strategies to access noncanonical α-amino acids. Chem Sci 2024; 15:5832-5868. [PMID: 38665517 PMCID: PMC11041364 DOI: 10.1039/d4sc01081g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Organocatalytic asymmetric synthesis has evolved over the years and continues to attract the interest of many researchers worldwide. Enantiopure noncanonical amino acids (ncAAs) are valuable building blocks in organic synthesis, medicinal chemistry, and chemical biology. They are employed in the elaboration of peptides and proteins with enhanced activities and/or improved properties compared to their natural counterparts, as chiral catalysts, in chiral ligand design, and as chiral building blocks for asymmetric syntheses of complex molecules, including natural products. The linkage of ncAA synthesis and enantioselective organocatalysis, the subject of this perspective, tries to imitate the natural biosynthetic process. Herein, we present contemporary and earlier developments in the field of organocatalytic activation of simple feedstock materials, providing potential ncAAs with diverse side chains, unique three-dimensional structures, and a high degree of functionality. These asymmetric organocatalytic strategies, useful for forging a wide range of C-C, C-H, and C-N bonds and/or combinations thereof, vary from classical name reactions, such as Ugi, Strecker, and Mannich reactions, to the most advanced concepts such as deracemisation, transamination, and carbene N-H insertion. Concurrently, we present some interesting mechanistic studies/models, providing information on the chirality transfer process. Finally, this perspective highlights, through the diversity of the amino acids (AAs) not selected by nature for protein incorporation, the most generic modes of activation, induction, and reactivity commonly used, such as chiral enamine, hydrogen bonding, Brønsted acids/bases, and phase-transfer organocatalysis, reflecting their increasingly important role in organic and applied chemistry.
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Affiliation(s)
- Pietro Pecchini
- Department of Industrial Chemistry "Toso Montanari", Center for Chemical Catalysis C3 & INSTM RU Bologna V. Gobetti 85 40129 Bologna Italy
| | - Mariafrancesca Fochi
- Department of Industrial Chemistry "Toso Montanari", Center for Chemical Catalysis C3 & INSTM RU Bologna V. Gobetti 85 40129 Bologna Italy
| | - Francesca Bartoccini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino PU Italy
| | - Giovanni Piersanti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino PU Italy
| | - Luca Bernardi
- Department of Industrial Chemistry "Toso Montanari", Center for Chemical Catalysis C3 & INSTM RU Bologna V. Gobetti 85 40129 Bologna Italy
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2
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Yu MZ, Yuan Y, Li ZJ, Kunthic T, Wang HX, Xu C, Xiang Z. An Artificial Enzyme for Asymmetric Nitrocyclopropanation of α,β-Unsaturated Aldehydes-Design and Evolution. Angew Chem Int Ed Engl 2024:e202401635. [PMID: 38597773 DOI: 10.1002/anie.202401635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/24/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024]
Abstract
The introduction of an abiological catalytic group into the binding pocket of a protein host allows for the expansion of enzyme chemistries. Here, we report the generation of an artificial enzyme by genetic encoding of a non-canonical amino acid that contains a secondary amine side chain. The non-canonical amino acid and the binding pocket function synergistically to catalyze the asymmetric nitrocyclopropanation of α,β-unsaturated aldehydes by the iminium activation mechanism. The designer enzyme was evolved to an optimal variant that catalyzes the reaction at high conversions with high diastereo- and enantioselectivity. This work demonstrates the application of genetic code expansion in enzyme design and expands the scope of enzyme-catalyzed abiological reactions.
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Affiliation(s)
- Ming-Zhu Yu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Ye Yuan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Zhen-Jie Li
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Nanshan District, 518055, Shenzhen, P. R. China
| | - Thittaya Kunthic
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - He-Xiang Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
| | - Chen Xu
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Nanshan District, 518055, Shenzhen, P. R. China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China
- Institute of Chemical Biology, Shenzhen Bay Laboratory Gaoke Innovation Center, Guangqiao Road, Guangming District, 518132, Shenzhen, P. R. China
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3
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Li Q, Wang H, Zhang W, Wang W, Ren X, Wu M, Shi G. Structure-Guided Evolution Modulate Alcohol Oxidase to Improve Ethanol Oxidation Performance. Appl Biochem Biotechnol 2024; 196:1948-1965. [PMID: 37453026 DOI: 10.1007/s12010-023-04626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
A high ethanol usage of alcohol oxidase (AOX) was required in industry. In this study, a "expand substrate pocket" strategy achieved a high activity AOX from Hansenula polymorpha (H. polymorpha) by Phe to Val residue (F/V) site-directed mutation to enlarge ethanol channel. Although H. Polymorpha AOX (HpAOX) possessed respectively 71.3% and 76.1% similarity with AOX (PpAOX) from Pichia pastoris (P. pastoris) in DNA and protein sequences, their active site structures including catalytic site and substrate channel were similar according to computer-aided analysis. After 3D structure analysis, Phe99 residue of their substrate channels was the most important residue to impact enzyme activity because of its large aromatic side chains. F99V mutation of HpAOX (HpAOXF99V) was designed and executed based on the enzyme catalytic mechanism and molecular computation in order to allow more larger size ethanol into active site. The highest enzyme activity of the fourth strains of HpAOXF99V mutant strain exhibited 12.06-folds increase than that of the host GS115 strain. Furthermore, kinetic studies indicated that the HpAOXF99V significantly promoted catalytic efficiency of ethanol than HpAOX, including Km, Vmax, kcat and kcat/Km. We also provided a new insight that the cofactor FAD irritated both active AOX octamer biosynthesis production and enzyme-catalysed ability due to help enzyme assembly and redox potential.
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Affiliation(s)
- Qian Li
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Haiou Wang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China.
| | - Wenxiao Zhang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Wenxuan Wang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xiaoyu Ren
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Mengyao Wu
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Guoqing Shi
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
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4
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Hossain MM, Shaikh AC, Kaur R, Gianetti TL. Red Light-Blue Light Chromoselective C(sp 2)-X Bond Activation by Organic Helicenium-Based Photocatalysis. J Am Chem Soc 2024; 146:7922-7930. [PMID: 38498938 DOI: 10.1021/jacs.3c13380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Chromoselective bond activation has been achieved in organic helicenium (nPr-DMQA+)-based photoredox catalysis. Consequently, control over chromoselective C(sp2)-X bond activation in multihalogenated aromatics has been demonstrated. nPr-DMQA+ can only initiate the halogen atom transfer (XAT) pathway under red light irradiation to activate low-energy-accessible C(sp2)-I bonds. In contrast, blue light irradiation initiates consecutive photoinduced electron transfer (conPET) to activate more challenging C(sp2)-Br bonds. Comparative reaction outcomes have been demonstrated in the α-arylation of cyclic ketones with red and blue lights. Furthermore, red-light-mediated selective C(sp2)-I bonds have been activated in iodobromoarenes to keep the bromo functional handle untouched. Finally, the strength of the chromoselective catalysis has been highlighted with two-fold functionalization using both photo-to-transition metal and photo-to-photocatalyzed transformations.
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Affiliation(s)
- Md Mubarak Hossain
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Aslam C Shaikh
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Ramandeep Kaur
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Thomas L Gianetti
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
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Li R, Yin S, Xie L, Li X, Jia J, Zhao L, He CY. Catalyst-free decarboxylative cross-coupling of N-hydroxyphthalimide esters with tert-butyl 2-(trifluoromethyl)acrylate and its application. Org Biomol Chem 2024; 22:2279-2283. [PMID: 38407278 DOI: 10.1039/d3ob02103c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Here, we demonstrate a practical method toward the facile synthesis of CF3-containing amino acids through visible light promoted decarboxylative cross-coupling of a redox-active ester with tert-butyl 2-(trifluoromethyl)acrylate. The reaction was driven by the photochemical activity of electron donor-acceptor (EDA) complexes that were formed by the non-covalent interaction between a Hantzsch ester and a redox-active ester. The advantages of this protocol are its synthetic simplicity, rich functional group tolerance, and a cost-effective reaction system.
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Affiliation(s)
- Rui Li
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Susu Yin
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Lang Xie
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xuefei Li
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jia Jia
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Liang Zhao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Chun-Yang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou, P.R. China
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6
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Wu T, Zhang H, Zhang P, James TD, Sun X. A Rationally Designed Prodrug for the Fluorogenic Labeling of Albumin and Theranostic Effects on Drug-Induced Liver Injury. Anal Chem 2024; 96:3498-3507. [PMID: 38363806 DOI: 10.1021/acs.analchem.3c05272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The development of small-molecular fluorogenic tools for the chemo-selective labeling of proteins in live cells is important for the evaluation of intracellular redox homeostasis. Dynamic imaging of human serum albumin (HSA), an antioxidant protein under oxidative stress with concomitant release of antioxidant drugs to maintain redox homeostasis, affords potential opportunities for disease diagnosis and treatment. In this work, we developed a nonfluorogenic prodrug named TPA-NAC, by introducing N-acetyl-l-cysteine (NAC) into a conjugated acceptor skeleton. Through combined thiol and amino addition, coupling with HSA results in fluorescence turn-on and drug release. It was reasoned that the restricted intramolecular motion of the probe under an HSA microenvironment after covalent bonding inhibited the nonradiative transitions. Furthermore, the biocompatibility and photochemical properties of TPA-NAC enabled it to image exogenous and endogenous HSA in living cells in a wash-free manner. Additionally, the released drug evoked upregulation of superoxide dismutase (SOD), which synergistically eliminated reactive oxygen species in a drug-induced liver injury model. This study provides insights into the design of new theranostic fluorescent prodrugs for chemo-selective protein labeling and disease treatments.
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Affiliation(s)
- Tianhong Wu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Hui Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Peng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Xiaolong Sun
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China
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7
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Reed JH, Seebeck FP. Reagent Engineering for Group Transfer Biocatalysis. Angew Chem Int Ed Engl 2024; 63:e202311159. [PMID: 37688533 DOI: 10.1002/anie.202311159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/11/2023]
Abstract
Biocatalysis has become a major driver in the innovation of preparative chemistry. Enzyme discovery, engineering and computational design have matured to reliable strategies in the development of biocatalytic processes. By comparison, substrate engineering has received much less attention. In this Minireview, we highlight the idea that the design of synthetic reagents may be an equally fruitful and complementary approach to develop novel enzyme-catalysed group transfer chemistry. This Minireview discusses key examples from the literature that illustrate how synthetic substrates can be devised to improve the efficiency, scalability and sustainability, as well as the scope of such reactions. We also provide an opinion as to how this concept might be further developed in the future, aspiring to replicate the evolutionary success story of natural group transfer reagents, such as adenosine triphosphate (ATP) and S-adenosyl methionine (SAM).
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Affiliation(s)
- John H Reed
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
- Molecular Systems Engineering, National Competence Center in Research, 4058, Basel, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
- Molecular Systems Engineering, National Competence Center in Research, 4058, Basel, Switzerland
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8
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Bilal M, Qamar SA, Carballares D, Berenguer-Murcia Á, Fernandez-Lafuente R. Proteases immobilized on nanomaterials for biocatalytic, environmental and biomedical applications: Advantages and drawbacks. Biotechnol Adv 2024; 70:108304. [PMID: 38135131 DOI: 10.1016/j.biotechadv.2023.108304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Proteases have gained significant scientific and industrial interest due to their unique biocatalytic characteristics and broad-spectrum applications in different industries. The development of robust nanobiocatalytic systems by attaching proteases onto various nanostructured materials as fascinating and novel nanocarriers has demonstrated exceptional biocatalytic performance, substantial stability, and ease of recyclability over multiple reaction cycles under different chemical and physical conditions. Proteases immobilized on nanocarriers may be much more resistant to denaturation caused by extreme temperatures or pH values, detergents, organic solvents, and other protein denaturants than free enzymes. Immobilized proteases may present a lower inhibition. The use of non-porous materials in the immobilization prevents diffusion and steric hindrances during the binding of the substrate to the active sites of enzymes compared to immobilization onto porous materials; when using very large or solid substrates, orientation of the enzyme must always be adequate. The advantages and problems of the immobilization of proteases on nanoparticles are discussed in this review. The continuous and batch reactor operations of nanocarrier-immobilized proteases have been successfully investigated for a variety of applications in the leather, detergent, biomedical, food, and pharmaceutical industries. Information about immobilized proteases on various nanocarriers and nanomaterials has been systematically compiled here. Furthermore, different industrial applications of immobilized proteases have also been highlighted in this review.
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Affiliation(s)
- Muhammad Bilal
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, G. Narutowicza 11/12 Str., 80-233 Gdansk, Poland; Advanced Materials Center, Gdansk University of Technology, 11/12 Narutowicza St., 80-233 Gdansk, Poland.
| | - Sarmad Ahmad Qamar
- Department of Environmental, Biological & Pharmaceutical Sciences, and Technologies, University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100 Caserta, Italy
| | - Diego Carballares
- Department of Biocatalysis, ICP-CSIC, C/ Marie Curie 2, Campus UAM-CSIC Cantoblanco, Madrid, Spain
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, 03080 Alicante, Spain
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9
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Hong H, Lee UJ, Lee SH, Kim H, Lim GM, Lee SH, Son HF, Kim BG, Kim KJ. Highly efficient site-specific protein modification using tyrosinase from Streptomyces avermitilis: Structural insight. Int J Biol Macromol 2024; 255:128313. [PMID: 37995783 DOI: 10.1016/j.ijbiomac.2023.128313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/19/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023]
Abstract
Tyrosinase-mediated protein conjugation has recently drawn attention as a site-specific protein modification tool under mild conditions. However, the tyrosinases reported to date act only on extremely exposed tyrosine residues, which limits where the target tyrosine can be located. Herein, we report a tyrosinase from Streptomyces avermitilis (SaTYR), that exhibits a much higher activity against tyrosine residues on the protein surface than other tyrosinases. We determined the crystal structure of SaTYR and revealed that the enzyme has a relatively flat and shallow substrate-binding pocket to accommodate a protein substrate. We demonstrated SaTYR-mediated fluorescence dye tagging and PEGylation of a surface tyrosine residue that was unreacted by other tyrosinases with an approximately 95.2 % conjugation yield in 1 h. We also present a structural rationale that considers the steric hindrance from adjacent residues and surrounding structures along with the extent of solvent exposure of residues, as necessary when determining the optimal positions for introducing target tyrosine residues in SaTYR-mediated protein modification. The study demonstrated that the novel tyrosinase, SaTYR, extends the scope of tyrosinase-mediated protein modification, and we propose that site-specific tyrosine conjugation using SaTYR is a promising strategy for protein bioconjugation in various applications.
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Affiliation(s)
- Hwaseok Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute of Microbiology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Uk-Jae Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX/N-Bio, Institute of BioEngineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute of Microbiology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX/N-Bio, Institute of BioEngineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Gyu-Min Lim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Hyuk Lee
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyeoncheol Francis Son
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX/N-Bio, Institute of BioEngineering, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute of Microbiology, Kyungpook National University, Daegu 41566, Republic of Korea.
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10
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Guo Y, Liu S, Jing D, Liu N, Luo X. The construction of elastin-like polypeptides and their applications in drug delivery system and tissue repair. J Nanobiotechnology 2023; 21:418. [PMID: 37951928 PMCID: PMC10638729 DOI: 10.1186/s12951-023-02184-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
Elastin-like polypeptides (ELPs) are thermally responsive biopolymers derived from natural elastin. These peptides have a low critical solution temperature phase behavior and can be used to prepare stimuli-responsive biomaterials. Through genetic engineering, biomaterials prepared from ELPs can have unique and customizable properties. By adjusting the amino acid sequence and length of ELPs, nanostructures, such as micelles and nanofibers, can be formed. Correspondingly, ELPs have been used for improving the stability and prolonging drug-release time. Furthermore, ELPs have widespread use in tissue repair due to their biocompatibility and biodegradability. Here, this review summarizes the basic property composition of ELPs and the methods for modulating their phase transition properties, discusses the application of drug delivery system and tissue repair and clarifies the current challenges and future directions of ELPs in applications.
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Affiliation(s)
- Yingshu Guo
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Shiwei Liu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Dan Jing
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Nianzu Liu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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11
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Bora JR, Mahalakshmi R. Empowering canonical biochemicals with cross-linked novelty: Recursions in applications of protein cross-links. Proteins 2023. [PMID: 37589191 DOI: 10.1002/prot.26571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023]
Abstract
Diversity in the biochemical workhorses of the cell-that is, proteins-is achieved by the innumerable permutations offered primarily by the 20 canonical L-amino acids prevalent in all biological systems. Yet, proteins are known to additionally undergo unusual modifications for specialized functions. Of the various post-translational modifications known to occur in proteins, the recently identified non-disulfide cross-links are unique, residue-specific covalent modifications that confer additional structural stability and unique functional characteristics to these biomolecules. We review an exclusive class of amino acid cross-links encompassing aromatic and sulfur-containing side chains, which not only confer superior biochemical characteristics to the protein but also possess additional spectroscopic features that can be exploited as novel chromophores. Studies of their in vivo reaction mechanism have facilitated their specialized in vitro applications in hydrogels and protein anchoring in monolayer chips. Furthering the discovery of unique canonical cross-links through new chemical, structural, and bioinformatics tools will catalyze the development of protein-specific hyperstable nanostructures, superfoods, and biotherapeutics.
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Affiliation(s)
- Jinam Ravindra Bora
- Department of Biological Sciences, Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Department of Biological Sciences, Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal, India
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12
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Ponzar N, Pozzi N. Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET. Methods 2023; 214:8-17. [PMID: 37068599 PMCID: PMC10203983 DOI: 10.1016/j.ymeth.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
Disulfide bonds drive protein correct folding, prevent protein aggregation, and stabilize three-dimensional structures of proteins and their assemblies. Dysregulation of this activity leads to several disorders, including cancer, neurodegeneration, and thrombosis. A family of 20+ enzymes, called thiol-isomerases (TIs), oversee this process in the endoplasmic reticulum of human cells to ensure efficacy and accuracy. While the biophysical and biochemical properties of cysteine residues are well-defined, our structural knowledge of how TIs select, interact and process their substrates remains poorly understood. How TIs structurally and functionally respond to changes in redox environment and other post-translational modifications remain unclear, too. We recently developed a workflow for site-specific incorporation of non-canonical amino acids into protein disulfide isomerase (PDI), the prototypical member of TIs. Combined with click chemistry, this strategy enabled us to perform single-molecule biophysical studies of PDI under various solution conditions. This paper details protocols and discusses challenges in performing these experiments. We expect this approach, combined with other emerging technologies in single-molecule biophysics and structural biology, to facilitate the exploration of the mechanisms by which TIs carry out their fascinating but poorly understood roles in humans, especially in the context of thrombosis.
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Affiliation(s)
- Nathan Ponzar
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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13
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Wang Z, Zhou M, Cao N, Wang X. Site-directed modification of multifunctional lignocellulose-degrading enzymes of straw based on homologous modeling. World J Microbiol Biotechnol 2023; 39:214. [PMID: 37256388 DOI: 10.1007/s11274-023-03663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
Studying the straw lignocellulose strengthening mechanism during simultaneous degradation has important practical significance for improving resource utilization and reducing environmental pollution. In this paper, the degradation ability of four straw lignocellulose-degrading enzymes was evaluated by molecular docking and molecular dynamics. Using the significantly binds to straw lignocellulose-degrading enzyme as a template, a multifunctional lignocellulose-degrading enzyme 3CBH-1KS5-4XQD-1B85 was constructed based on amino acid recombination and homologous modeling. Five efficient degrading enzymes (3CBH-1, 3CBH-2, 3CBH-3, 3CBH-4, and 3CBH-5) were designed by site-directed mutagenesis of 3CBH-1KS5-4XQD-1B85 amino acid at position 346. Molecular dynamics showed that the degradation ability of 3CBH-1 was significant and it was 1.45 times higher than 3CBH-1KS5-4XQD-1B85. Moreover, the mechanism of enhanced degradability and the stability of the enzymes were explored. With the aid of Taguchi experiments, the suitable external environment for degrading straw was determined. In the presence of inhibitors (organic acids and phenolic compounds), the binding energy of 3CBH-1 (238.46 ± 30.96 kJ/mol) is 36.42% higher than that of 3CBH-1KS5-4XQD-1B85 (174.79 ± 20.35 kJ/mol) without external environmental stimulation. Based on homology modeling, this paper constructed a site-directed mutagenesis scheme of multifunctional enzymes, and the aim was to obtain multifunctional and efficient straw lignocellulose-degrading enzymes through protein engineering, which provided a feasible scheme for straw biodegradation.
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Affiliation(s)
- Zini Wang
- College of Plant Science, Jilin University, 5333 Xian Road, Changchun, 130062, China
| | - Mengying Zhou
- China Guangdong Nuclear Research Institute Limited Company, 1001 Shangbu Middle Road, Shenzhen, 518000, China
| | - Ning Cao
- College of Plant Science, Jilin University, 5333 Xian Road, Changchun, 130062, China
| | - Xiaoli Wang
- College of Plant Science, Jilin University, 5333 Xian Road, Changchun, 130062, China.
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14
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Mohite P, Shah SR, Singh S, Rajput T, Munde S, Ade N, Prajapati BG, Paliwal H, Mori DD, Dudhrejiya AV. Chitosan and chito-oligosaccharide: a versatile biopolymer with endless grafting possibilities for multifarious applications. Front Bioeng Biotechnol 2023; 11:1190879. [PMID: 37274159 PMCID: PMC10235636 DOI: 10.3389/fbioe.2023.1190879] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Chito-oligosaccharides (COS), derived from chitosan (CH), are attracting increasing attention as drug delivery carriers due to their biocompatibility, biodegradability, and mucoadhesive properties. Grafting, the process of chemically modifying CH/COS by adding side chains, has been used to improve their drug delivery performance by enhancing their stability, targeted delivery, and controlled release. In this review, we aim to provide an in-depth study on the recent advances in the grafting of CH/COS for multifarious applications. Moreover, the various strategies and techniques used for grafting, including chemical modification, enzymatic modification, and physical modification, are elaborated. The properties of grafted CH/COS, such as stability, solubility, and biocompatibility, were reported. Additionally, the review detailed the various applications of grafted CH/COS in drug delivery, including the delivery of small drug molecule, proteins, and RNA interference therapeutics. Furthermore, the effectiveness of grafted CH/COS in improving the pharmacokinetics and pharmacodynamics of drugs was included. Finally, the challenges and limitations associated with the use of grafted CH/COS for drug delivery and outline directions for future research are addressed. The insights provided in this review will be valuable for researchers and drug development professionals interested in the application of grafted CH/COS for multifarious applications.
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Affiliation(s)
- Popat Mohite
- AETs St. John Institute of Pharmacy and Research, Palghar, Maharashtra, India
| | - Sunny R. Shah
- B. K. Mody Government Pharmacy College, Gujarat Technological University, Rajkot, India
| | - Sudarshan Singh
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand
| | - Tanavirsing Rajput
- AETs St. John Institute of Pharmacy and Research, Palghar, Maharashtra, India
| | - Shubham Munde
- AETs St. John Institute of Pharmacy and Research, Palghar, Maharashtra, India
| | - Nitin Ade
- AETs St. John Institute of Pharmacy and Research, Palghar, Maharashtra, India
| | - Bhupendra G. Prajapati
- Shree S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, India
| | - Himanshu Paliwal
- Drug Delivery System Excellence Centre, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Dhaval D. Mori
- B. K. Mody Government Pharmacy College, Gujarat Technological University, Rajkot, India
| | - Ashvin V. Dudhrejiya
- B. K. Mody Government Pharmacy College, Gujarat Technological University, Rajkot, India
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15
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Fu M, Cao Z, Sun R, Wen X, Wang Y, Li K, Li Q. Maleic anhydride promotes humus formation via inducing functional enzymes response in composting. BIORESOURCE TECHNOLOGY 2023; 380:129125. [PMID: 37127171 DOI: 10.1016/j.biortech.2023.129125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
The purpose of this paper was to explore the promotion of maleic anhydride on the polymerization of precursors into humus in composting, and analyze the changes of key functional enzymes. The results showed that the content of humus in the treatment group added maleic anhydride (MAH) was higher than that in the control check (CK). The decrease rate of humus precursor concentration of MAH was also higher than that of CK. In MAH, the activities of laccase and tyrosinase were improved, thus enhanced the catalytic conversion of humus precursors. The analysis of bacterial community showed that maleic anhydride optimized the community structure of humification functional enzymes producing bacteria, with the most obvious increase of Firmicutes. In conclusion, this study provided theoretical supports for the introduction of maleic anhydride into the compost system to promote the polymerization of precursors to form humus.
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Affiliation(s)
- Mengxin Fu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Ziyi Cao
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Ru Sun
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xiaoli Wen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yiwu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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16
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Guo H, Sun N, Guo J, Zhou TP, Tang L, Zhang W, Deng Y, Liao RZ, Wu Y, Wu G, Zhong F. Expanding the Promiscuity of a Copper-Dependent Oxidase for Enantioselective Cross-Coupling of Indoles. Angew Chem Int Ed Engl 2023; 62:e202219034. [PMID: 36789864 DOI: 10.1002/anie.202219034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/16/2023]
Abstract
Herein, we disclose the highly enantioselective oxidative cross-coupling of 3-hydroxyindole esters with various nucleophilic partners as catalyzed by copper efflux oxidase. The biocatalytic transformation delivers functionalized 2,2-disubstituted indolin-3-ones with excellent optical purity (90-99 % ee), which exhibited anticancer activity against MCF-7 cell lines, as shown by preliminary biological evaluation. Mechanistic studies and molecular docking results suggest the formation of a phenoxyl radical and enantiocontrol facilitated by a suited enzyme chiral pocket. This study is significant with regard to expanding the catalytic repertoire of natural multicopper oxidases as well as enlarging the synthetic toolbox for sustainable asymmetric oxidative coupling.
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Affiliation(s)
- Huan Guo
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Ningning Sun
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Juan Guo
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Tai-Ping Zhou
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Langyu Tang
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Wentao Zhang
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Yaming Deng
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Rong-Zhen Liao
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Yuzhou Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Guojiao Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Fangrui Zhong
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
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17
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Insertion of unnatural metal ligand in the heme pocket of nitrophorin through protein semi-synthesis: toward biomimicking binuclear active sites. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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18
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Wang J, Xia Y, Guo X. Repurposing Photosensitizer Proteins Through Genetic Code Expansion to Facilitate Photo-Biocatalysis. Methods Mol Biol 2023; 2676:41-54. [PMID: 37277623 DOI: 10.1007/978-1-0716-3251-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Artificial photoenzymes with noncanonical photo-redox cofactors have paved the way for enzyme rational design and the creation of new-to-nature biocatalysts. Genetically encoded photo-redox cofactors endow photoenzymes with enhanced or novel activities that catalyze numerous transformations with high efficiency. Herein, we describe a protocol of repurposing photosensitizer proteins (PSP) through genetic code expansion to facilitate multiple photocatalytic conversions including photo-activated dehalogenation of aryl halides, CO2 to CO and CO2 to formic acid reduction. The methods for expression, purification, and characterization of the PSP are detailed. The installation of the catalytic modules and the utilization of PSP-based artificial photoenzymes for photoenzymatic CO2 reduction and dehalogenation are also described.
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Affiliation(s)
- Jiangyun Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
| | - Yan Xia
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xuzhen Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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19
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Bedendi G, De Moura Torquato LD, Webb S, Cadoux C, Kulkarni A, Sahin S, Maroni P, Milton RD, Grattieri M. Enzymatic and Microbial Electrochemistry: Approaches and Methods. ACS MEASUREMENT SCIENCE AU 2022; 2:517-541. [PMID: 36573075 PMCID: PMC9783092 DOI: 10.1021/acsmeasuresciau.2c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 06/17/2023]
Abstract
The coupling of enzymes and/or intact bacteria with electrodes has been vastly investigated due to the wide range of existing applications. These span from biomedical and biosensing to energy production purposes and bioelectrosynthesis, whether for theoretical research or pure applied industrial processes. Both enzymes and bacteria offer a potential biotechnological alternative to noble/rare metal-dependent catalytic processes. However, when developing these biohybrid electrochemical systems, it is of the utmost importance to investigate how the approaches utilized to couple biocatalysts and electrodes influence the resulting bioelectrocatalytic response. Accordingly, this tutorial review starts by recalling some basic principles and applications of bioelectrochemistry, presenting the electrode and/or biocatalyst modifications that facilitate the interaction between the biotic and abiotic components of bioelectrochemical systems. Focus is then directed toward the methods used to evaluate the effectiveness of enzyme/bacteria-electrode interaction and the insights that they provide. The basic concepts of electrochemical methods widely employed in enzymatic and microbial electrochemistry, such as amperometry and voltammetry, are initially presented to later focus on various complementary methods such as spectroelectrochemistry, fluorescence spectroscopy and microscopy, and surface analytical/characterization techniques such as quartz crystal microbalance and atomic force microscopy. The tutorial review is thus aimed at students and graduate students approaching the field of enzymatic and microbial electrochemistry, while also providing a critical and up-to-date reference for senior researchers working in the field.
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Affiliation(s)
- Giada Bedendi
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | | | - Sophie Webb
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Amogh Kulkarni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Selmihan Sahin
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Plinio Maroni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Matteo Grattieri
- Dipartimento
di Chimica, Università degli Studi
di Bari “Aldo Moro”, via E. Orabona 4, Bari 70125, Italy
- IPCF-CNR
Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, via E. Orabona 4, Bari 70125, Italy
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20
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Akram F, Aqeel A, Shoaib M, Haq IU, Shah FI. Multifarious revolutionary aspects of microbial keratinases: an efficient green technology for future generation with prospective applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:86913-86932. [PMID: 36271998 DOI: 10.1007/s11356-022-23638-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Since the dawn of century, tons of keratin bio-waste is generated by the poultry industry annually, and they end up causing environmental havoc. Keratins are highly flexible fibrous proteins which exist in α- and β- forms and provide mechanical strength and stability to structural appendages. The finding of broad-spectrum protease, keratinase, from thermophilic bacteria and fungi, has provided an eco-friendly solution to hydrolyze the peptide bonds in highly recalcitrant keratinous substances such as nails, feathers, claws, and horns into valuable amino acids. Microorganisms produce these proteolytic enzymes by techniques of solid-state and submerged fermentation. However, solid-state fermentation is considered as a yielding approach for the production of thermostable keratinases. This review prioritized the molecular and biochemical properties of microbial keratinases, and the role of keratinases in bringing prodigious impact for the sustainable progress of the economy. It also emphasizes on the current development in keratinase production with the focus to improve the biochemical properties related to enzyme's catalytic activity and stability, and production of mutant and cloned microbial strains to improve the yield of keratinases. Recently, multitude molecular approaches have been employed to enhance enzyme's productivity, activity, and thermostability which makes them suitable for pharmaceutical industry and for the production of animal feed, organic fertilizers, biogas, clearing of animal hides, and detergent formulation. Hence, it can be surmised that microbial keratinolytic enzymes are the conceivable candidates for numerous commercial and industrial applications.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Minahil Shoaib
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
- Pakistan Academy of Science, Islamabad, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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21
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Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling. Commun Biol 2022; 5:1254. [DOI: 10.1038/s42003-022-04141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractActivity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.
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22
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Birch-Price Z, Taylor CJ, Ortmayer M, Green AP. Engineering enzyme activity using an expanded amino acid alphabet. Protein Eng Des Sel 2022; 36:6825271. [PMID: 36370045 PMCID: PMC9863031 DOI: 10.1093/protein/gzac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/01/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022] Open
Abstract
Enzyme design and engineering strategies are typically constrained by the limited size of nature's genetic alphabet, comprised of only 20 canonical amino acids. In recent years, site-selective incorporation of non-canonical amino acids (ncAAs) via an expanded genetic code has emerged as a powerful means of inserting new functional components into proteins, with hundreds of structurally diverse ncAAs now available. Here, we highlight how the emergence of an expanded repertoire of amino acids has opened new avenues in enzyme design and engineering. ncAAs have been used to probe complex biological mechanisms, augment enzyme function and, most ambitiously, embed new catalytic mechanisms into protein active sites that would be challenging to access within the constraints of nature's genetic code. We predict that the studies reviewed in this article, along with further advances in genetic code expansion technology, will establish ncAA incorporation as an increasingly important tool for biocatalysis in the coming years.
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Affiliation(s)
- Zachary Birch-Price
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Christopher J Taylor
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Mary Ortmayer
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
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23
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Ji X, Zhu N, Ma Y, Liu J, Hu Y. Protein C-Terminal Tyrosine Conjugation via Recyclable Immobilized BmTYR. ACS OMEGA 2022; 7:40532-40539. [PMID: 36385814 PMCID: PMC9647846 DOI: 10.1021/acsomega.2c05794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Protein modification plays an essential role in biological and pharmaceutical research. Due to the ordinary selectivity and inevitable damage to proteins of chemical synthetic methods, increased efforts were focused on biocatalysts which exhibited high regioselectivity and mild reaction conditions. However, separation of the biocatalysts and modified proteins remained a problem, especially when scaling up. Here, we developed a simple method for site-specific protein modification with a recyclable biocatalyst. The immobilizing tyrosinase (BmTYR) on magnetic beads can oxidize C-terminal tyrosine residues of the target protein to o-quinone, followed by the spontaneous addition of different nucleophiles (e.g., aniline derivatives), resulting in a C-terminal modified protein. Compared to the homogeneous biocatalytic system reported before, this heterogeneous system leads to an easier separation. Furthermore, the solid-phase biocatalyst can be regenerated during separation, providing reusability and lower costs.
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Affiliation(s)
- Xingyu Ji
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia, Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Nanlin Zhu
- Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Yanjie Ma
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia, Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jia Liu
- Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 310024, China
| | - Youhong Hu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia, Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 310024, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
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24
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Koch NG, Baumann T, Nickling JH, Dziegielewski A, Budisa N. Engineered bacterial host for genetic encoding of physiologically stable protein nitration. Front Mol Biosci 2022; 9:992748. [PMID: 36353730 PMCID: PMC9638147 DOI: 10.3389/fmolb.2022.992748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
Across scales, many biological phenomena, such as protein folding or bioadhesion and cohesion, rely on synergistic effects of different amino acid side chains at multiple positions in the protein sequence. These are often fine-tuned by post-translational modifications that introduce additional chemical properties. Several PTMs can now be genetically encoded and precisely installed at single and multiple sites by genetic code expansion. Protein nitration is a PTM of particular interest because it has been associated with several diseases. However, even when these nitro groups are directly incorporated into proteins, they are often physiologically reduced during or shortly after protein production. We have solved this problem by using an engineered Escherichia coli host strain. Six genes that are associated with nitroreductase activity were removed from the genome in a simple and robust manner. The result is a bacterial expression host that can stably produce proteins and peptides containing nitro groups, especially when these are amenable to modification. To demonstrate the applicability of this strain, we used this host for several applications. One of these was the multisite incorporation of a photocaged 3,4-dihydroxyphenylalanine derivative into Elastin-Like Polypeptides. For this non-canonical amino acid and several other photocaged ncAAs, the nitro group is critical for photocleavability. Accordingly, our approach also enhances the production of biomolecules containing photocaged tyrosine in the form of ortho-nitrobenzyl-tyrosine. We envision our engineered host as an efficient tool for the production of custom designed proteins, peptides or biomaterials for various applications ranging from research in cell biology to large-scale production in biotechnology.
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Affiliation(s)
- Nikolaj G. Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jessica H. Nickling
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Anna Dziegielewski
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Chemical Synthetic Biology Group, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Nediljko Budisa,
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25
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Jeon H, Pagar AD, Kang H, Giri P, Nadarajan SP, Sarak S, Khobragade TP, Lim S, Patil MD, Lee SG, Yun H. Creation of a ( R)-β-Transaminase by Directed Evolution of d-Amino Acid Aminotransferase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hyunwoo Jeon
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Amol D. Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Hyeona Kang
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Saravanan P. Nadarajan
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Sharad Sarak
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Taresh P. Khobragade
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Seonga Lim
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D. Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali, Punjab 140306, India
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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26
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Morellon-Sterling R, Bolivar JM, Fernandez-Lafuente R. Switch off/switch on of a cysteinyl protease as a way to preserve the active catalytic group by modification with a reversible covalent thiol modifier: Immobilization of ficin on vinyl-sulfone activated supports. Int J Biol Macromol 2022; 220:1155-1162. [PMID: 36037909 DOI: 10.1016/j.ijbiomac.2022.08.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/11/2022] [Accepted: 08/23/2022] [Indexed: 11/05/2022]
Abstract
The immobilization of ficin (a cysteinyl proteases) on vinyl sulfone agarose produced its almost full inactivation. It was observed that the incubation of the free and immobilized enzyme in β-mercaptoethanol produced a 20 % of enzyme activity recovery, suggesting that the inactivation due to the immobilization could be a consequence of the modification of the catalytic Cys. To prevent the enzyme inactivation during the immobilization, switching off of ficin via Cys reaction with dipyridyl-disulfide was implemented, giving a reversible disulfide bond that produced a fully inactive enzyme. The switch on of ficin activity was implemented by incubation in 1 M β-mercaptoethanol. Using this strategy to immobilize the enzyme on vinyl sulfone agarose beads, the expressed activity of the immobilized ficin could be boosted up to 80 %. The immobilized enzyme presented a thermal stabilization similar to that obtained using ficin-glyoxyl-agarose beads. This procedure may be extended to many enzymes containing critical Cys, to permit their immobilization or chemical modification.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Juan M Bolivar
- FQPIMA Group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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27
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Bolivar JM, Woodley JM, Fernandez-Lafuente R. Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization. Chem Soc Rev 2022; 51:6251-6290. [PMID: 35838107 DOI: 10.1039/d2cs00083k] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.
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Affiliation(s)
- Juan M Bolivar
- FQPIMA group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, 28040, Spain
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC, C/Marie Curie 2, Campus UAM-CSIC Cantoblanco, Madrid 28049, Spain. .,Center of Excellence in Bionanoscience Research, External Scientific Advisory Academic, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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28
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Kinetic model for reversible radical transfer in ribonucleotide reductase. Proc Natl Acad Sci U S A 2022; 119:e2202022119. [PMID: 35714287 DOI: 10.1073/pnas.2202022119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.
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29
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Chen N, Chang B, Shi N, Yan W, Lu F, Liu F. Cross-linked enzyme aggregates immobilization: preparation, characterization, and applications. Crit Rev Biotechnol 2022; 43:369-383. [PMID: 35430938 DOI: 10.1080/07388551.2022.2038073] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are commonly used as biocatalysts for various biological and chemical processes. However, some major drawbacks of free enzymes (e.g. poor reusability and instability) significantly restrict their industrial practices. How to overcome these weaknesses remain considerable challenges. Enzyme immobilization is one of the most effective ways to improve the reusability and stability of enzymes. Cross-linked enzyme aggregates (CLEAs) has been known as a novel and versatile carrier-free immobilization method. CLEAs is attractive due to its simplicity and robustness, without purification. It generally shows: high catalytic specificity and selectivity, good operational and storage stabilities, and good reusability. Moreover, co-immobilization of different kinds of enzymes can be acquired. These CLEAs advantages provide opportunities for further industrial applications. Herein, the preparation parameters of CLEAs were first summarized. Next, characterization of structural and catalytic properties, stability and reusability are also proposed. Finally, some important applications of this technique in: environmental protection, industrial chemistry, food industry, and pharmaceutical synthesis and delivery are introduced. Potential challenges and future research directions, such as improving cross-linking efficiency and internal mass transfer efficiency, are also presented. This implies that CLEAs provide an efficient and feasible technique to improve the properties of enzymes for use in the industry.
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Affiliation(s)
- Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P. R. China
| | - Baogen Chang
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P. R. China
| | - Nian Shi
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P. R. China
| | - Wenxing Yan
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P. R. China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P. R. China
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30
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Naapuri JM, Losada-Garcia N, Deska J, Palomo JM. Synthesis of silver and gold nanoparticles-enzyme-polymer conjugate hybrids as dual-activity catalysts for chemoenzymatic cascade reactions. NANOSCALE 2022; 14:5701-5715. [PMID: 35343986 DOI: 10.1039/d2nr00361a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Novel hybrids containing silver or gold nanoparticles have been synthesized in aqueous media and at room temperature using enzymes or tailor-made enzyme-polymer conjugates, which directly induced the formation of inorganic silver or gold species. The choice of pH, protein, or bioconjugate strongly affected the final metallic nanoparticles hybrid formation. Using Candida antarctica lipase (CALB) in a solution, nanobiohybrids containing Ag2O nanoparticles of 9 nm average diameter were obtained. The use of tailor-made bioconjugates, for example, the CALB modified with dextran-aspartic acid polymer (Dext6kDa), resulted in a nanobiohybrid containing smaller Ag(0)/Ag2O nanoparticles. In the case of nanobiohybrids based on gold, Au(0) species were found in all cases. The Au-CALB hybrid contained spherical nanoparticles with 18 nm average diameter size, with a minor range of larger ones (>100 nm) while the AuNPs-CALB-Dext6kDa hybrid was formed by much smaller nanoparticles (9 nm, minor range of 22 nm), and also nanorods of 20-30/40-50 nm length. Using Thermomyces lanuginosus lipase (TLL), apart from the nanoparticle formation, nanoflowers with a diameter range of 100-200 nm were obtained. All nanobiohybrids maintained (dual) enzymatic and metallic activities. For instance, these nanobiohybrids exhibited exquisite dual-activity for hydrolysis/cycloisomerization cascades starting from allenic acetates. By merging the transition metal reactivity with the inherent lipase catalysis, allenic acetates directly converted to the corresponding O-heterocycles in enantiopure form catalysed by AgNPs-CALB-Dext6kDa, taking advantage of a kinetic resolution/cyclization pathway. These results showed the high applicability of these novel hybrids, offering new opportunities for the design of novel reaction cascades.
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Affiliation(s)
- Janne M Naapuri
- Department of Biocatalysis, Institute of Catalysis (ICP-CSIC), Marie Curie 2, 28049 Madrid, Spain.
- Department of Chemistry, University of Helsinki, A. I. Virtasen aukio 1, 00560 Helsinki, Finland.
- Department of Chemistry, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Noelia Losada-Garcia
- Department of Biocatalysis, Institute of Catalysis (ICP-CSIC), Marie Curie 2, 28049 Madrid, Spain.
| | - Jan Deska
- Department of Chemistry, University of Helsinki, A. I. Virtasen aukio 1, 00560 Helsinki, Finland.
- Department of Chemistry, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Jose M Palomo
- Department of Biocatalysis, Institute of Catalysis (ICP-CSIC), Marie Curie 2, 28049 Madrid, Spain.
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31
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Hadar D, Strugach DS, Amiram M. Conjugates of Recombinant Protein‐Based Polymers: Combining Precision with Chemical Diversity. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202100142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
| | - Daniela S. Strugach
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev P.O. Box 653 Beer-Sheva 8410501 Israel
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32
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Pagar AD, Jeon H, Khobragade TP, Sarak S, Giri P, Lim S, Yoo TH, Ko BJ, Yun H. Non-Canonical Amino Acid-Based Engineering of (R)-Amine Transaminase. Front Chem 2022; 10:839636. [PMID: 35295971 PMCID: PMC8918476 DOI: 10.3389/fchem.2022.839636] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 01/07/2023] Open
Abstract
Non-canonical amino acids (ncAAs) have been utilized as an invaluable tool for modulating the active site of the enzymes, probing the complex enzyme mechanisms, improving catalytic activity, and designing new to nature enzymes. Here, we report site-specific incorporation of p-benzoyl phenylalanine (pBpA) to engineer (R)-amine transaminase previously created from d-amino acid aminotransferase scaffold. Replacement of the single Phe88 residue at the active site with pBpA exhibits a significant 15-fold and 8-fold enhancement in activity for 1-phenylpropan-1-amine and benzaldehyde, respectively. Reshaping of the enzyme’s active site afforded an another variant F86A/F88pBpA, with 30% higher thermostability at 55°C without affecting parent enzyme activity. Moreover, various racemic amines were successfully resolved by transaminase variants into (S)-amines with excellent conversions (∼50%) and enantiomeric excess (>99%) using pyruvate as an amino acceptor. Additionally, kinetic resolution of the 1-phenylpropan-1-amine was performed using benzaldehyde as an amino acceptor, which is cheaper than pyruvate. Our results highlight the utility of ncAAs for designing enzymes with enhanced functionality beyond the limit of 20 canonical amino acids.
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Affiliation(s)
- Amol D. Pagar
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Hyunwoo Jeon
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | | | - Sharad Sarak
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Pritam Giri
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Seonga Lim
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women’s University, Seoul, South Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
- *Correspondence: Hyungdon Yun,
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33
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You S, Ruan M, Lu C, Liu L, Weng Y, Yang G, Wang S, Alhumade H, Lei A, Gao M. Paired electrolysis enabled annulation for the quinolyl-modification of bioactive molecules. Chem Sci 2022; 13:2310-2316. [PMID: 35310496 PMCID: PMC8864700 DOI: 10.1039/d1sc06757e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/26/2022] [Indexed: 12/15/2022] Open
Abstract
A paired electrolysis enabled cascade annulation that enables the efficient synthesis of highly functionalized quinoline-substituted bioactive molecules from readily available starting materials is reported. Using this methodology, two goals, namely, the direct synthesis of quinolines and the introduction of quinoline moieties to bioactive molecules, can be simultaneously achieved in one simple operation. The use of electroreduction for the activation of isatin, together with the further anodic oxidation of KI to catalytically result in a cascade annulation, highlight the unique possibilities associated with electrochemical activation methods. This transformation can tolerate a wide range of functional groups and can also be used as a functionalization tactic in pharmaceutical research as well as other areas. A paired electrolysis enabled cascade annulation that enables the efficient synthesis of highly functionalized quinoline-substituted bioactive molecules from readily available starting materials is reported.![]()
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Affiliation(s)
- Shiqi You
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
| | - Mengyao Ruan
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
| | - Cuifen Lu
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
| | - Li Liu
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
| | - Yue Weng
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
| | - Guichun Yang
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
| | - Shengchun Wang
- College of Chemistry and Molecular Sciences and the Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 Hubei P. R. China
| | - Hesham Alhumade
- Department of Chemical and Materials Engineering, Faculty of Engineering, Center of Research Excellence in Renewable Energy and Power Systems, King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Aiwen Lei
- College of Chemistry and Molecular Sciences and the Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 Hubei P. R. China .,Department of Chemical and Materials Engineering, Faculty of Engineering, Center of Research Excellence in Renewable Energy and Power Systems, King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Meng Gao
- College of Chemistry and Chemical Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University Wuhan 430062 P. R. China
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Chemical modification for improving catalytic performance of lipase B from Candida antarctica with hydrophobic proline ionic liquid. Bioprocess Biosyst Eng 2022; 45:749-759. [PMID: 35113231 DOI: 10.1007/s00449-022-02696-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022]
Abstract
In this study, a series of proline ionic liquids with different lengths of hydrophobic alkyl on the side chain were used to modify the Candida Antarctic lipase B (CALB). The catalytic activity, thermal stability and tolerance to methanol and DMSO of the modified enzyme were all improved simultaneously. The optimum temperature changed from 55 to 60 ℃. The hydrophobicity and anion type of the modifier have important influence on the catalytic performance of CALB. CALB modified by [ProC12][H2PO4] has a better effect. Under the optimal conditions, its hydrolysis activity was 3.0 times than that of the native enzyme, the catalytic efficiency Kcat/Km improved 2.8 times in aqueous phase, and the tolerance to organic solvent with strong polarity (50% methanol 2 h) was increased by 6.8 times. Fluorescence spectra and circular dichroism (CD) spectroscopy showed that the introduction of ionic liquids changed the microenvironment near the fluorophores of the enzyme protein, the α-helix decreased and β-sheet increased in the secondary structure of the modified enzymes. The root mean square deviation (RMSD), residue root mean square fluctuation (RMSF), radius of gyration (Rg), and solution accessible surface area (SASA) of [ProC2][Br]-CALB, [ProC12][Br]-CALB and native CALB were obtained for comparison by molecular dynamics simulation. The results of dynamics simulation were in good agreement with enzymology experiment. The introduction of ionic liquids can keep CALB in a better active conformation, and proline ionic liquids with long hydrophobic chains can significantly improve the surface hydrophobicity and overall rigidity of CALB. This research offers a new idea for rapid screening of efficient modifiers and provision of enzymes with high stability and activity for industrial application.
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35
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Han LL, Zhang QY, Li X, Qiao Y, Lan Y, Wei D. The chiral pyridoxal-catalyzed biomimetic Mannich reaction: the mechanism and origin of stereoselectivity. Org Chem Front 2022. [DOI: 10.1039/d2qo00705c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A biomimetic organocatalyst with a pyridoxal-like structure is one of the most successful examples of catalyzing organic reactions under mild conditions in an asymmetric synthesis field.
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Affiliation(s)
- Li-Li Han
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Qiao-Yu Zhang
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Xue Li
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
| | - Yu Lan
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Donghui Wei
- Green Catalysis Center and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
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36
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Gou FH, Ma MJ, Wang AJ, Zhao L, Wang H, Tong J, Wang Z, Wang Z, He CY. Nickel-Catalyzed Cross-Coupling of Amino-Acid-Derived Alkylzinc Reagents with Alkyl Bromides/Chlorides: Access to Diverse Unnatural Amino Acids. Org Lett 2021; 24:240-244. [PMID: 34958223 DOI: 10.1021/acs.orglett.1c03884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Unnatural α-amino acids are important synthetic targets in the field of peptide science. Herein we report an efficient, versatile, and straightforward strategy for the synthesis of homophenylalanine derivatives via the nickel-catalyzed Csp3-Csp3 cross-coupling of (fluoro)benzyl bromides/chlorides with natural α-amino-acid-derived alkylzinc reagents. The current protocol features the advantages of a low-cost nickel catalyst system, synthetic convenience, and the tolerance of rich functionality and stereochemistry.
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Affiliation(s)
- Fei-Hu Gou
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ming-Jian Ma
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - An-Jun Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Liang Zhao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Haoyang Wang
- Laboratory of Mass Spectrometry Analysis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Tong
- School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Ze Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zhen Wang
- School of Pharmaceutical Science, University of South China, Hengyang 421001, China
| | - Chun-Yang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
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37
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Protein Modifications: From Chemoselective Probes to Novel Biocatalysts. Catalysts 2021. [DOI: 10.3390/catal11121466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chemical reactions can be performed to covalently modify specific residues in proteins. When applied to native enzymes, these chemical modifications can greatly expand the available set of building blocks for the development of biocatalysts. Nucleophilic canonical amino acid sidechains are the most readily accessible targets for such endeavors. A rich history of attempts to design enhanced or novel enzymes, from various protein scaffolds, has paved the way for a rapidly developing field with growing scientific, industrial, and biomedical applications. A major challenge is to devise reactions that are compatible with native proteins and can selectively modify specific residues. Cysteine, lysine, N-terminus, and carboxylate residues comprise the most widespread naturally occurring targets for enzyme modifications. In this review, chemical methods for selective modification of enzymes will be discussed, alongside with examples of reported applications. We aim to highlight the potential of such strategies to enhance enzyme function and create novel semisynthetic biocatalysts, as well as provide a perspective in a fast-evolving topic.
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38
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Giri P, Pagar AD, Patil MD, Yun H. Chemical modification of enzymes to improve biocatalytic performance. Biotechnol Adv 2021; 53:107868. [PMID: 34774927 DOI: 10.1016/j.biotechadv.2021.107868] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022]
Abstract
Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.
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Affiliation(s)
- Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mahesh D Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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39
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Lee BS, Choi WJ, Lee SW, Ko BJ, Yoo TH. Towards Engineering an Orthogonal Protein Translation Initiation System. Front Chem 2021; 9:772648. [PMID: 34765589 PMCID: PMC8576571 DOI: 10.3389/fchem.2021.772648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
In the last two decades, methods to incorporate non-canonical amino acids (ncAAs) into specific positions of a protein have advanced significantly; these methods have become general tools for engineering proteins. However, almost all these methods depend on the translation elongation process, and strategies leveraging the initiation process have rarely been reported. The incorporation of a ncAA specifically at the translation initiation site enables the installation of reactive groups for modification at the N-termini of proteins, which are attractive positions for introducing abiological groups with minimal structural perturbations. In this study, we attempted to engineer an orthogonal protein translation initiation system. Introduction of the identity elements of Escherichia coli initiator tRNA converted an engineered Methanococcus jannaschii tRNATyr into an initiator tRNA. The engineered tRNA enabled the site-specific incorporation of O-propargyl-l-tyrosine (OpgY) into the amber (TAG) codon at the translation initiation position but was inactive toward the elongational TAG codon. Misincorporation of Gln was detected, and the engineered system was demonstrated only with OpgY. We expect further engineering of the initiator tRNA for improved activity and specificity to generate an orthogonal translation initiation system.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Woon Jong Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sang Woo Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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40
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Pan X, Yang J, Xie P, Zhang J, Ke F, Guo X, Liang M, Liu L, Wang Q, Gao X. Enhancement of Activity and Thermostability of Keratinase From Pseudomonas aeruginosa CCTCC AB2013184 by Directed Evolution With Noncanonical Amino Acids. Front Bioeng Biotechnol 2021; 9:770907. [PMID: 34733836 PMCID: PMC8558439 DOI: 10.3389/fbioe.2021.770907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
A keratinase from Pseudomonas aeruginosa (KerPA), which belongs to the M4 family of metallopeptidases, was characterised in this study. This enzyme was engineered with non-canonical amino acids (ncAAs) using genetic code expansion. Several variants with enhanced activity and thermostability were identified and the most prominent, Y21pBpF/Y70pBpF/Y114pBpF, showed an increase in enzyme activity and half-life of approximately 1.3-fold and 8.2-fold, respectively. Considering that keratinases usually require reducing agents to efficiently degrade keratin, the Y21pBpF/Y70pBpF/Y114pBpF variant with enhanced activity and stability under reducing conditions may have great significance for practical applications. Molecular Dynamics (MD) was performed to identify the potential mechanisms underlying these improvements. The results showed that mutation with pBpF at specific sites of the enzyme could fill voids, form new interactions, and reshape the local structure of the active site of the enzyme.
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Affiliation(s)
- Xianchao Pan
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jian Yang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Peijuan Xie
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jing Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Famin Ke
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiurong Guo
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Manyu Liang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Li Liu
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiaowei Gao
- School of Pharmacy, Southwest Medical University, Luzhou, China.,Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Department of Chemistry, Zhejiang University, Hangzhou, China
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41
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Ebensperger P, Jessen-Trefzer C. Artificial metalloenzymes in a nutshell: the quartet for efficient catalysis. Biol Chem 2021; 403:403-412. [PMID: 34653321 DOI: 10.1515/hsz-2021-0329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
Artificial metalloenzymes combine the inherent reactivity of transition metal catalysis with the sophisticated reaction control of natural enzymes. By providing new opportunities in bioorthogonal chemistry and biocatalysis, artificial metalloenzymes have the potential to overcome certain limitations in both drug discovery and green chemistry or related research fields. Ongoing advances in organometallic catalysis, directed evolution, and bioinformatics are enabling the design of increasingly powerful systems that outperform conventional catalysis in a growing number of cases. Therefore, this review article collects challenges and opportunities in designing artificial metalloenzymes described in recent review articles. This will provide an equitable insight for those new to and interested in the field.
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Affiliation(s)
- Paul Ebensperger
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
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42
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Kim S, Yi H, Kim YT, Lee HS. Engineering Translation Components for Genetic Code Expansion. J Mol Biol 2021; 434:167302. [PMID: 34673113 DOI: 10.1016/j.jmb.2021.167302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/26/2021] [Accepted: 10/05/2021] [Indexed: 12/18/2022]
Abstract
The expansion of the genetic code consisting of four bases and 20 amino acids into diverse building blocks has been an exciting topic in synthetic biology. Many biochemical components are involved in gene expression; therefore, adding a new component to the genetic code requires engineering many other components that interact with it. Genetic code expansion has advanced significantly for the last two decades with the engineering of several components involved in protein synthesis. These components include tRNA/aminoacyl-tRNA synthetase, new codons, ribosomes, and elongation factor Tu. In addition, biosynthesis and enhanced uptake of non-canonical amino acids have been attempted and have made meaningful progress. This review discusses the efforts to engineer these translation components, to improve the genetic code expansion technology.
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Affiliation(s)
- Sooin Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Hanbin Yi
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Yurie T Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea.
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43
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Koch NG, Goettig P, Rappsilber J, Budisa N. Engineering Pyrrolysyl-tRNA Synthetase for the Incorporation of Non-Canonical Amino Acids with Smaller Side Chains. Int J Mol Sci 2021; 22:11194. [PMID: 34681855 PMCID: PMC8538471 DOI: 10.3390/ijms222011194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Site-specific incorporation of non-canonical amino acids (ncAAs) into proteins has emerged as a universal tool for systems bioengineering at the interface of chemistry, biology, and technology. The diversification of the repertoire of the genetic code has been achieved for amino acids with long and/or bulky side chains equipped with various bioorthogonal tags and useful spectral probes. Although ncAAs with relatively small side chains and similar properties are of great interest to biophysics, cell biology, and biomaterial science, they can rarely be incorporated into proteins. To address this gap, we report the engineering of PylRS variants capable of incorporating an entire library of aliphatic "small-tag" ncAAs. In particular, we performed mutational studies of a specific PylRS, designed to incorporate the shortest non-bulky ncAA (S-allyl-l-cysteine) possible to date and based on this knowledge incorporated aliphatic ncAA derivatives. In this way, we have not only increased the number of translationally active "small-tag" ncAAs, but also determined key residues responsible for maintaining orthogonality, while engineering the PylRS for these interesting substrates. Based on the known plasticity of PylRS toward different substrates, our approach further expands the reassignment capacities of this enzyme toward aliphatic amino acids with smaller side chains endowed with valuable functionalities.
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Affiliation(s)
- Nikolaj G. Koch
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany;
- Institut für Biotechnologie-Bioanalytik, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria;
| | - Juri Rappsilber
- Institut für Biotechnologie-Bioanalytik, Technische Universität Berlin, 10623 Berlin, Germany;
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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44
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Khobragade TP, Sarak S, Pagar AD, Jeon H, Giri P, Yun H. Synthesis of Sitagliptin Intermediate by a Multi-Enzymatic Cascade System Using Lipase and Transaminase With Benzylamine as an Amino Donor. Front Bioeng Biotechnol 2021; 9:757062. [PMID: 34692666 PMCID: PMC8526967 DOI: 10.3389/fbioe.2021.757062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/21/2021] [Indexed: 01/30/2023] Open
Abstract
Herein, we report the development of a multi-enzyme cascade using transaminase (TA), esterase, aldehyde reductase (AHR), and formate dehydrogenase (FDH), using benzylamine as an amino donor to synthesize the industrially important compound sitagliptin intermediate. A panel of 16 TAs was screened using ethyl 3-oxo-4-(2,4,5-trifluorophenyl) butanoate as a substrate (1). Amongst these enzymes, TA from Roseomonas deserti (TARO) was found to be the most suitable, showing the highest activity towards benzylamine (∼70%). The inhibitory effect of benzaldehyde was resolved by using AHR from Synechocystis sp. and FDH from Pseudomonas sp., which catalyzed the conversion of benzaldehyde to benzyl alcohol at the expense of NAD(P)H. Reaction parameters, such as pH, buffer system, and concentration of amino donor, were optimized. A single whole-cell system was developed for co-expressing TARO and esterase, and the promoter engineering strategy was adopted to control the expression level of each biocatalyst. The whole-cell reactions were performed with varying substrate concentrations (10-100 mM), resulting in excellent conversions (ranging from 72 to 91%) into the desired product. Finally, the applicability of this cascade was highlighted on Gram scale, indicating production of 70% of the sitagliptin intermediate with 61% isolated yield. The protocol reported herein may be considered an alternative to existing methods with respect to the use of cheaper amine donors as well as improved synthesis of (R) and (S) enantiomers with the use of non-chiral amino donors.
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Affiliation(s)
| | | | | | | | | | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
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45
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Imam HT, Krasňan V, Rebroš M, Marr AC. Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis. Molecules 2021; 26:4791. [PMID: 34443378 PMCID: PMC8399596 DOI: 10.3390/molecules26164791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.
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Affiliation(s)
- Hasan Tanvir Imam
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
| | - Vladimír Krasňan
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Andrew Craig Marr
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
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46
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Bora HJ, Barman P, Bordoloi S, Gogoi G, Gogoi B, Sen Sarma N, Kalita A. Realization of multi-configurable logic gate behaviour on fluorescence switching signalling of naphthalene diimide congeners. RSC Adv 2021; 11:35274-35279. [PMID: 35493194 PMCID: PMC9043018 DOI: 10.1039/d1ra06728a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/17/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022] Open
Abstract
Organic entities like suitably functionalized naphthalene diimide (NDI) exhibited logical behaviours in response to various external stimuli and can be used to develop digital logic operations. The present findings include utilization of two congeners of NDI i.e., N1 and N2 for the successive turning ON/OFF of fluorescence with inclusion of acid and base. The recognition of the switching phenomenon of the probes N1 and N2 are applied to construct fundamental digital logic gates such as NOT, YES, IMPLICATION, INHIBIT, etc. The inputs to each of the logic gates are defined by the presence or absence of acid and base. Accordingly, the outputs generated from the gates are in the form of fluorescence ON or OFF status denoted by “1” and “0” respectively. Likewise, we have adopted Boolean algebra and its associated De-Morgan's theorem to build the combined logic gates such as XOR and XNOR gates. The proposed logic gates are validated by the optical behaviour of the congeners N1 and N2 in response to acid as well as base and the experimental results are confirmed by the theoretical predictions. The proposed work can have potential applications in next-generation logic based analytical applications. The implementation of functional congeners of naphthalene diimide experiencing fluorescence ON/OFF switching signalling in response to external stimuli, is suitably realized to construct multi-configurable molecular logic gates.![]()
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Affiliation(s)
- Hridoy Jyoti Bora
- Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-781035, Assam, India
| | - Pranjal Barman
- Department of Electronics and Communication Technology, Gauhati University, Guwahati-781014, Assam, India
| | - Sushanta Bordoloi
- Department of Electronics and Communication Engineering, National Institute of Technology Mizoram, Aizawl-796012, India
| | - Gautomi Gogoi
- Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-781035, Assam, India
| | - Bedanta Gogoi
- Department of Chemistry, Gauhati University, Guwahati-781014, Assam, India
| | - Neelotpal Sen Sarma
- Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-781035, Assam, India
| | - Anamika Kalita
- Physical Sciences Division, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-781035, Assam, India
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