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Jørgensen FK, Delcey MG, Hedegård ED. Perspective: multi-configurational methods in bio-inorganic chemistry. Phys Chem Chem Phys 2024; 26:17443-17455. [PMID: 38868993 DOI: 10.1039/d4cp01297f] [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: 06/14/2024]
Abstract
Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the electronic structure and properties of metalloproteins poses significant challenges due to the complex nature of their electronic configurations and strong correlation effects. Multiconfigurational quantum chemistry methods are, in principle, the most appropriate tools for addressing these challenges, offering the capability to capture the inherent multi-reference character and strong electron correlation present in bio-inorganic systems. Yet their computational cost has long hindered wider adoption, making methods such as density functional theory (DFT) the method of choice. However, advancements over the past decade have substantially alleviated this limitation, rendering multiconfigurational quantum chemistry methods more accessible and applicable to a wider range of bio-inorganic systems. In this perspective, we discuss some of these developments and how they have already been used to answer some of the most important questions in bio-inorganic chemistry. We also comment on ongoing developments in the field and how the future of the field may evolve.
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Affiliation(s)
- Frederik K Jørgensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Mickaël G Delcey
- Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Erik D Hedegård
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
- Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00 Lund, Sweden
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2
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Gao W, Li T, Zhou H, Ju J, Yin H. Carbohydrate-binding modules enhance H 2O 2 tolerance by promoting lytic polysaccharide monooxygenase active site H 2O 2 consumption. J Biol Chem 2024; 300:105573. [PMID: 38122901 PMCID: PMC10825053 DOI: 10.1016/j.jbc.2023.105573] [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: 09/12/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) oxidatively depolymerize recalcitrant polysaccharides, which is important for biomass conversion. The catalytic domains of many LPMOs are linked to carbohydrate-binding modules (CBMs) through flexible linkers, but the function of these CBMs in LPMO catalysis is not well understood. In this study, we utilized MtLPMO9L and MtLPMO9G derived from Myceliophthora thermophila to investigate the impact of CBMs on LPMO activity, with particular emphasis on their influence on H2O2 tolerance. Using truncated forms of MtLPMO9G generated by removing the CBM, we found reduced substrate binding affinity and enzymatic activity. Conversely, when the CBM was fused to the C terminus of the single-domain MtLPMO9L to create MtLPMO9L-CBM, we observed a substantial improvement in substrate binding affinity, enzymatic activity, and notably, H2O2 tolerance. Furthermore, molecular dynamics simulations confirmed that the CBM fusion enhances the proximity of the active site to the substrate, thereby promoting multilocal cleavage and impacting the exposure of the copper active site to H2O2. Importantly, the fusion of CBM resulted in more efficient consumption of H2O2 by LPMO, leading to improved enzymatic activity and reduced auto-oxidative damage of the copper active center.
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Affiliation(s)
- Wa Gao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tang Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haichuan Zhou
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jiu Ju
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese Academy of Sciences, Beijing, China.
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3
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Guo X, Jiang L, An Y, Lu F, Liu F, Wang B. Construction and characterization of a Myceliophthora thermophila lytic polysaccharide monooxygenase mutant S174C/A93C with improved thermostability. Enzyme Microb Technol 2023; 168:110255. [PMID: 37178549 DOI: 10.1016/j.enzmictec.2023.110255] [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: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) can oxidatively cleave the glycosidic bonds of crystalline polysaccharides, providing more accessible sites for polysaccharide hydrolases and promoting efficient conversion of biomass. In order to promote industrial applications of LPMOs, the stability of an LPMO of Myceliophthora thermophila C1 (MtC1LPMO) was improved by adding disulfide bonds in this study. Firstly, the structural changes of wild-type (WT) MtC1LPMO at different temperatures were explored using molecular dynamics simulations, and eight mutants were selected by combining the predicted results from Disulfide by Design (DBD), Multi agent stability prediction upon point mutations (Maestro) and Bridge disulfide (BridgeD) websites. Then, the enzymatic properties of the different mutants were determined after their expression and purification, and the mutant S174C/A93C with the highest thermal stability was obtained. The specific activities of unheated S174C/A93C and WT were 160.6 ± 1.7 U/g and 174.8 ± 7.5 U/g, respectively, while those of S174C/A93C and WT treated at 70 °C for 4 h were 77.7 ± 3.4 U/g and 46.1 ± 0.4 U/g, respectively. The transition midpoint temperature of S174C/A93C was 2.7 °C higher than that of WT. The conversion efficiency of S174C/A93C for both microcrystalline cellulose and corn straw was about 1.5 times higher than that of WT. Finally, molecular dynamics simulations revealed that the introduction of disulfide bonds increased the β-sheet content of the H1-E34 region, thus improving the rigidity of the protein. Therefore, the overall structural stability of S174C/A93C was improved, which in turn improved its thermal stability.
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Affiliation(s)
- Xiao Guo
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Yajing An
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China.
| | - Bo Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China.
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4
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Hagemann MM, Hedegård ED. Molecular Mechanism of Substrate Oxidation in Lytic Polysaccharide Monooxygenases: Insight from Theoretical Investigations. Chemistry 2023; 29:e202202379. [PMID: 36207279 PMCID: PMC10107554 DOI: 10.1002/chem.202202379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that today comprise a large enzyme superfamily, grouped into the distinct members AA9-AA17 (with AA12 exempted). The LPMOs have the potential to facilitate the upcycling of biomass waste products by boosting the breakdown of cellulose and other recalcitrant polysaccharides. The cellulose biopolymer is the main component of biomass waste and thus comprises a large, unexploited resource. The LPMOs work through a catalytic, oxidative reaction whose mechanism is still controversial. For instance, the nature of the intermediate performing the oxidative reaction is an open question, and the same holds for the employed co-substrate. Here we review theoretical investigations addressing these questions. The applied theoretical methods are usually based on quantum mechanics (QM), often combined with molecular mechanics (QM/MM). We discuss advantages and disadvantages of the employed theoretical methods and comment on the interplay between theoretical and experimental results.
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Affiliation(s)
- Marlisa M Hagemann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Erik D Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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5
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Zhang H, Zhou H, Zhao Y, Li T, Yin H. Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis. PeerJ 2023; 11:e14670. [PMID: 36684673 PMCID: PMC9851047 DOI: 10.7717/peerj.14670] [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: 09/21/2022] [Accepted: 12/09/2022] [Indexed: 01/19/2023] Open
Abstract
Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B.
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Affiliation(s)
- Huiyan Zhang
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haichuan Zhou
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yong Zhao
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tang Li
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Heng Yin
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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6
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Synergic chitin degradation by Streptomyces sp. SCUT-3 chitinases and their applications in chitinous waste recycling and pathogenic fungi biocontrol. Int J Biol Macromol 2023; 225:987-996. [PMID: 36403764 DOI: 10.1016/j.ijbiomac.2022.11.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022]
Abstract
The genus Streptomyces comprises the most important chitin decomposers in soil and revealing their chitinolytic machinery is beneficial for the conversion of chitinous wastes. Streptomyces sp. SCUT-3, a chitin-hydrolyzing and a robust feather-degrading bacterium, was isolated previously. The potential chitin-degrading enzymes produced by SCUT-3 were analyzed in the present study. Among these enzymes, three chitinases were successfully expressed in Pichia pastoris at comparatively high yields of 4.8 U/mL (SsExoChi18A), 11.2 U/mL (SsExoChi18B), and 17.8 U/mL (SsEndoChi19). Conserved motifs and constructive 3D structures of these three exo- and endochitinases were also analyzed. These chitinases hydrolyzed colloidal chitin to chitin oligomers. SsExoChi18A showed apparent synergic effects with SsEndoChi19 in colloidal chitin and shrimp shell hydrolysis, with an improvement of 29.3 % and 124.9 %, respectively. Compared with SsExoChi18B and SsEndoChi19, SsExoChi18A exhibited the strongest antifungal effects against four plant pathogens by inhibiting mycelial growth and spore germination. This study provided good candidates for chitinous waste-processing enzymes and antifungal biocontrol agents. These synergic chitin-degrading enzymes of SCUT-3 are good targets for its further genetical modification to construct super chitinous waste-degrading bacteria with strong abilities to hydrolyze both protein and chitin, thereby providing a direction for the future path of the chitinous waste recycling industry.
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7
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Controlled depolymerization of cellulose by photoelectrochemical bioreactor using a lytic polysaccharide monooxygenase. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Guo X, An Y, Liu F, Lu F, Wang B. Lytic polysaccharide monooxygenase - A new driving force for lignocellulosic biomass degradation. BIORESOURCE TECHNOLOGY 2022; 362:127803. [PMID: 35995343 DOI: 10.1016/j.biortech.2022.127803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) can catalyze polysaccharides by oxidative cleavage of glycosidic bonds and have catalytic activity for cellulose, hemicellulose, chitin, starch and pectin, thus playing an important role in the biomass conversion of lignocellulose. The catalytic substrates of LPMOs are different and the specific catalytic mechanism has not been fully elucidated. Although there have been many studies related to LPMOs, few have actually been put into industrial biomass conversion, which poses a challenge for their expression, regulation and application. In this review, the origin, substrate specificity, structural features, and the relationship between structure and function of LPMOs are described. Additionally, the catalytic mechanism and electron donor of LPMOs and their heterologous expression and regulation are discussed. Finally, the synergistic degradation of biomass by LPMOs with other polysaccharide hydrolases is reviewed, and their current problems and future research directions are pointed out.
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Affiliation(s)
- Xiao Guo
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Yajing An
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Bo Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China.
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9
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Long L, Hu Y, Sun F, Gao W, Hao Z, Yin H. Advances in lytic polysaccharide monooxygenases with the cellulose-degrading auxiliary activity family 9 to facilitate cellulose degradation for biorefinery. Int J Biol Macromol 2022; 219:68-83. [PMID: 35931294 DOI: 10.1016/j.ijbiomac.2022.07.240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/18/2022]
Abstract
One crucial step in processing the recalcitrant lignocellulosic biomass is the fast hydrolysis of natural cellulose to fermentable sugars that can be subsequently converted to biofuels and bio-based chemicals. Recent studies have shown that lytic polysaccharide monooxygenase (LPMOs) with auxiliary activity family 9 (AA9) are capable of efficiently depolymerizing the crystalline cellulose via regioselective oxidation reaction. Intriguingly, the catalysis by AA9 LPMOs requires reductant to provide electrons, and lignin and its phenolic derivatives can be oxidized, releasing reductant to activate the reaction. The activity of AA9 LPMOs can be enhanced by in-situ generation of H2O2 in the presence of O2. Although scientific understanding of these enzymes remains somewhat unknown or controversial, structure modifications on AA9 LPMOs through protein engineering have emerged in recent years, which are prerequisite for their extensive applications in the development of cellulase-mediated lignocellulosic biorefinery processes. In this review, we critically comment on advances in studies for AA9 LPMOs, i.e., characteristic of AA9 LPMOs catalysis, external electron donors to AA9 LPMOs, especially the role of the oxidization of lignin and its derivatives, and AA9 LPMOs protein engineering as well as their extensive applications in the bioprocessing of lignocellulosic biomass. Perspectives are also highlighted for addressing the challenges.
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Affiliation(s)
- Lingfeng Long
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Wa Gao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
| | - Zhikui Hao
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou 318000, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
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Luo H, Liu X, Yu D, Yuan J, Tan J, Li H. Research Progress on Lignocellulosic Biomass Degradation Catalyzed by Enzymatic Nanomaterials. Chem Asian J 2022; 17:e202200566. [PMID: 35862657 DOI: 10.1002/asia.202200566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Indexed: 11/11/2022]
Abstract
Lignocellulose biomass (LCB) has extensive applications in many fields such as bioenergy, food, medicines, and raw materials for producing value-added products. One of the keys to efficient utilization of LCB is to obtain directly available oligo- and monomers (e.g., glucose). With the characteristics of easy recovery and separation, high efficiency, economy, and environmental protection, immobilized enzymes have been developed as heterogeneous catalysts to degrade LCB effectively. In this review, applications and mechanisms of LCB-degrading enzymes are discussed, and the nanomaterials and methods used to immobilize enzymes are also discussed. Finally, the research progress of lignocellulose biodegradation catalyzed by nano-enzymes was discussed.
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Affiliation(s)
- Hangyu Luo
- Guiyang University, College of Biology and Environmental Engineering, CHINA
| | - Xiaofang Liu
- Guiyang University, College of Biology and Environmental Engineering, CHINA
| | - Dayong Yu
- Guiyang University, College of Biology and Environmental Engineering, CHINA
| | - Junfa Yuan
- Guizhou University, Center for R&D of Fine Chemicals, CHINA
| | - Jinyu Tan
- Guizhou University, Center for R&D of Fine Chemicals, CHINA
| | - Hu Li
- Guizhou University, Center for R&D of Fine Chemicals, Huaxi Street, 550025, Guiyang, CHINA
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11
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Hellmers J, Hedegård ED, König C. Fragmentation-Based Decomposition of a Metalloenzyme-Substrate Interaction: A Case Study for a Lytic Polysaccharide Monooxygenase. J Phys Chem B 2022; 126:5400-5412. [PMID: 35833656 DOI: 10.1021/acs.jpcb.2c02883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel decomposition scheme for electronic interaction energies based on the flexible formulation of fragmentation schemes through fragment combination ranges (FCRs; J. Chem. Phys., 2021, 155, 164105). We devise a clear additive decomposition with contribution of nondisjoint fragments and correction terms for overlapping fragments and apply this scheme to the metalloenzyme-substrate complex of a lytic polysaccharide monooxygenase (LPMO) with an oligosaccharide. By this, we further illustrate the straightforward adaptability of the FCR-based schemes to novel systems. Our calculations suggest that the description of the electronic structure is a larger error source than the fragmentation scheme. In particular, we find a large impact of the basis set size on the interaction energies. Still, the introduction of three-body interaction terms in the fragmentation setup improves the agreement to the supermolecular reference. Yet, the qualitative results for the decomposition scheme with two-body terms only largely agree within the investigated electronic-structure approaches and basis sets, which are B97-3c, DFT (TPSS and B3LYP), and MP2 methods. The overlap contributions are found to be small, allowing analysis of the interaction energy into individual amino acid residues: We find a particularly strong interaction between the substrate and the LPMO copper active site.
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Affiliation(s)
- Janine Hellmers
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, 30167 Hannover, Germany
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, 30167 Hannover, Germany
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Theoretical perspective on mononuclear copper-oxygen mediated C–H and O–H activations: A comparison between biological and synthetic systems. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)63974-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Wang Z, Fang W, Peng W, Wu P, Wang B. Recent Computational Insights into the Oxygen Activation by Copper-Dependent Metalloenzymes. Top Catal 2022. [DOI: 10.1007/s11244-021-01444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Quantifying Oxidation of Cellulose-Associated Glucuronoxylan by Two Lytic Polysaccharide Monooxygenases from Neurospora crassa. Appl Environ Microbiol 2021; 87:e0165221. [PMID: 34613755 PMCID: PMC8612270 DOI: 10.1128/aem.01652-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Family AA9 lytic polysaccharide monooxygenases (LPMOs) are abundant in fungi, where they catalyze oxidative depolymerization of recalcitrant plant biomass. These AA9 LPMOs cleave cellulose and some also act on hemicelluloses, primarily other (substituted) β-(1→4)-glucans. Oxidative cleavage of xylan has been shown for only a few AA9 LPMOs, and it remains unclear whether this activity is a minor side reaction or primary function. Here, we show that Neurospora crassa LPMO9F (NcLPMO9F) and the phylogenetically related, hitherto uncharacterized NcLPMO9L from N. crassa are active on both cellulose and cellulose-associated glucuronoxylan but not on glucuronoxylan alone. A newly developed method for simultaneous quantification of xylan-derived and cellulose-derived oxidized products showed that NcLPMO9F preferentially cleaves xylan when acting on a cellulose–beechwood glucuronoxylan mixture, yielding about three times more xylan-derived than cellulose-derived oxidized products. Interestingly, under similar conditions, NcLPMO9L and the previously characterized McLPMO9H, from Malbranchea cinnamomea, showed different xylan-to-cellulose preferences, giving oxidized product ratios of about 0.5:1 and 1:1, respectively, indicative of functional variation among xylan-active LPMOs. Phylogenetic and structural analysis of xylan-active AA9 LPMOs led to the identification of characteristic structural features, including unique features that do not occur in phylogenetically remote AA9 LPMOs, such as four AA9 LPMOs whose lack of activity toward glucuronoxylan was demonstrated in the present study. Taken together, the results provide a path toward discovery of additional xylan-active LPMOs and show that the huge family of AA9 LPMOs has members that preferentially act on xylan. These findings shed new light on the biological role and industrial potential of these fascinating enzymes. IMPORTANCE Plant cell wall polysaccharides are highly resilient to depolymerization by hydrolytic enzymes, partly due to cellulose chains being tightly packed in microfibrils that are covered by hemicelluloses. Lytic polysaccharide monooxygenases (LPMOs) seem well suited to attack these resilient copolymeric structures, but the occurrence and importance of hemicellulolytic activity among LPMOs remain unclear. Here, we show that certain AA9 LPMOs preferentially cleave xylan when acting on a cellulose–glucuronoxylan mixture, and that this ability is the result of protein evolution that has resulted in a clade of AA9 LPMOs with specific structural features. Our findings strengthen the notion that the vast arsenal of AA9 LPMOs in certain fungal species provides functional versatility and that AA9 LPMOs may have evolved to promote oxidative depolymerization of a wide variety of recalcitrant, copolymeric plant polysaccharide structures. These findings have implications for understanding the biological roles and industrial potential of LPMOs.
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15
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Kuusk S, Väljamäe P. Kinetics of H 2O 2-driven catalysis by a lytic polysaccharide monooxygenase from the fungus Trichoderma reesei. J Biol Chem 2021; 297:101256. [PMID: 34597668 PMCID: PMC8528726 DOI: 10.1016/j.jbc.2021.101256] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 01/17/2023] Open
Abstract
Owing to their ability to break glycosidic bonds in recalcitrant crystalline polysaccharides such as cellulose, the catalysis effected by lytic polysaccharide monooxygenases (LPMOs) is of major interest. Kinetics of these reductant-dependent, monocopper enzymes is complicated by the insoluble nature of the cellulose substrate and parallel, enzyme-dependent, and enzyme-independent side reactions between the reductant and oxygen-containing cosubstrates. Here, we provide kinetic characterization of cellulose peroxygenase (oxidative cleavage of glycosidic bonds in cellulose) and reductant peroxidase (oxidation of the reductant) activities of the LPMO TrAA9A of the cellulose-degrading model fungus Trichoderma reesei. The catalytic efficiency (kcat/Km(H2O2)) of the cellulose peroxygenase reaction (kcat = 8.5 s−1, and Km(H2O2)=30μM) was an order of magnitude higher than that of the reductant (ascorbic acid) peroxidase reaction. The turnover of H2O2 in the ascorbic acid peroxidase reaction followed the ping-pong mechanism and led to irreversible inactivation of the enzyme with a probability of 0.0072. Using theoretical analysis, we suggest a relationship between the half-life of LPMO, the values of kinetic parameters, and the concentrations of the reactants.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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16
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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17
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Hedison TM, Breslmayr E, Shanmugam M, Karnpakdee K, Heyes DJ, Green AP, Ludwig R, Scrutton NS, Kracher D. Insights into the H 2 O 2 -driven catalytic mechanism of fungal lytic polysaccharide monooxygenases. FEBS J 2021; 288:4115-4128. [PMID: 33411405 PMCID: PMC8359147 DOI: 10.1111/febs.15704] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Fungal lytic polysaccharide monooxygenases (LPMOs) depolymerise crystalline cellulose and hemicellulose, supporting the utilisation of lignocellulosic biomass as a feedstock for biorefinery and biomanufacturing processes. Recent investigations have shown that H2O2 is the most efficient cosubstrate for LPMOs. Understanding the reaction mechanism of LPMOs with H2O2 is therefore of importance for their use in biotechnological settings. Here, we have employed a variety of spectroscopic and biochemical approaches to probe the reaction of the fungal LPMO9C from N. crassa using H2O2 as a cosubstrate and xyloglucan as a polysaccharide substrate. We show that a single ‘priming’ electron transfer reaction from the cellobiose dehydrogenase partner protein supports up to 20 H2O2‐driven catalytic cycles of a fungal LPMO. Using rapid mixing stopped‐flow spectroscopy, alongside electron paramagnetic resonance and UV‐Vis spectroscopy, we reveal how H2O2 and xyloglucan interact with the enzyme and investigate transient species that form uncoupled pathways of NcLPMO9C. Our study shows how the H2O2 cosubstrate supports fungal LPMO catalysis and leaves the enzyme in the reduced Cu+ state following a single enzyme turnover, thus preventing the need for external protons and electrons from reducing agents or cellobiose dehydrogenase and supporting the binding of H2O2 for further catalytic steps. We observe that the presence of the substrate xyloglucan stabilises the Cu+ state of LPMOs, which may prevent the formation of uncoupled side reactions.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Erik Breslmayr
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Photon Science Institute, The University of Manchester, UK
| | - Kwankao Karnpakdee
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Derren J Heyes
- Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Daniel Kracher
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
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18
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Lytic polysaccharide monooxygenases and other histidine-brace copper proteins: structure, oxygen activation and biotechnological applications. Biochem Soc Trans 2021; 49:531-540. [PMID: 33449071 PMCID: PMC7924993 DOI: 10.1042/bst20201031] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mononuclear copper enzymes that catalyse the oxidative cleavage of glycosidic bonds. They are characterised by two histidine residues that coordinate copper in a configuration termed the Cu-histidine brace. Although first identified in bacteria and fungi, LPMOs have since been found in all biological kingdoms. LPMOs are now included in commercial enzyme cocktails used in industrial biorefineries. This has led to increased process yield due to the synergistic action of LPMOs with glycoside hydrolases. However, the introduction of LPMOs makes control of the enzymatic step in industrial stirred-tank reactors more challenging, and the operational stability of the enzymes is reduced. It is clear that much is still to be learned about the interaction between LPMOs and their complex natural and industrial environments, and fundamental scientific studies are required towards this end. Several atomic-resolution structures have been solved providing detailed information on the Cu-coordination sphere and the interaction with the polysaccharide substrate. However, the molecular mechanisms of LPMOs are still the subject of intense investigation; the key question being how the proteinaceous environment controls the copper cofactor towards the activation of the O-O bond in O2 and cleavage of the glycosidic bonds in polysaccharides. The need for biochemical characterisation of each putative LPMO is discussed based on recent reports showing that not all proteins with a Cu-histidine brace are enzymes.
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19
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Guo X, An Y, Chai C, Sang J, Jiang L, Lu F, Dai Y, Liu F. Construction of the R17L mutant of MtC1LPMO for improved lignocellulosic biomass conversion by rational point mutation and investigation of the mechanism by molecular dynamics simulations. BIORESOURCE TECHNOLOGY 2020; 317:124024. [PMID: 32836036 DOI: 10.1016/j.biortech.2020.124024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
To enhance the biomass conversion efficiency, the R17L mutant of the lytic polysaccharide monooxygenase (LPMO) MtC1LPMO with improved catalytic efficiency was constructed via rational point mutation based on the HotSpot Wizard 3.0 and dezyme web servers. Compared with the wild-type (WT) MtC1LPMO, R17L exhibited a 1.8-fold increase of specific activity and 1.92-fold increase of catalytic efficiency (kcat/Km). The degree of increase of the reducing sugar yield from microcrystalline cellulose and three plant biomass materials during synergistic hydrolysis using cellulase in combination with R17L was about 2 times higher than with the WT. Molecular dynamics simulations revealed that the R17L mutation reduced the stability of the region R18-I36, which then weakened the direct interactions between region N24-V31 and the substrate cellohexaose. Consequently, the deflection time of the cellohexaose conformation in R17L was prolonged compared to the WT, which enhanced its catalytic efficiency.
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Affiliation(s)
- Xiao Guo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yajing An
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Chengcheng Chai
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Jingcheng Sang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yujie Dai
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China.
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20
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2020; 60:2385-2392. [DOI: 10.1002/anie.202011408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/05/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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21
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Wang B, Wang Z, Davies GJ, Walton PH, Rovira C. Activation of O2 and H2O2 by Lytic Polysaccharide Monooxygenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02914] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martı́ i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08020 Barcelona, Spain
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