1
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Jiang F, Wang Z, Cong Z. Tuning the peroxidase activity of artificial P450 peroxygenase by engineering redox-sensitive residues. Faraday Discuss 2024. [PMID: 38836616 DOI: 10.1039/d4fd00008k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Cytochrome P450 monooxygenases (P450s) are well recognized as versatile bio-oxidation catalysts. However, the catalytic functions of P450s are highly dependent on NAD(P)H and redox partner proteins. Our group has recently reported the use of a dual-functional small molecule (DFSM) for generating peroxygenase activity of P450BM3, a long-chain fatty acid hydroxylase from Bacillus megaterium. The DFSM-facilitated P450BM3 peroxygenase system exhibited excellent peroxygenation activity and regio-/enantioselectivity for various organic substrates, such as styrenes, thioanisole, small alkanes, and alkylbenzenes. Very recently, we demonstrated that the DFSM-facilitated P450BM3 peroxygenase could be switched to a peroxidase by engineering the redox-sensitive tyrosine residues in P450BM3. Given the great potential of P450 peroxidase for C-H oxyfunctionalization, we herein report scrutiny of the effect of mutating redox-sensitive residues on peroxidase activity by deeply screening all redox-sensitive residues of P450BM3, namely methionines, tryptophans, cysteines, and phenylalanines. As a result, six beneficial mutations at positions M212, F81, M112, F173, M177, and F77 were screened out from 78 constructed mutants, and significantly enhanced the peroxidase activity of P450BM3 in the presence of Im-C6-Phe, a typical DFSM molecule. Further combination of the beneficial mutations resulted in a more than 100-fold improvement in peroxidase activity compared with that of the combined parent enzyme and DFSM, comparable to or better than most natural peroxidases. In addition, mutations of redox-sensitive residues even dramatically increased, by more than 300-fold, the peroxidase activity of the starting F87A enzyme in the absence of the DFSM, despite the far lower apparent catalytic turnover number compared with the DFSM-P450 system. This study provides new insights and a potential strategy for regulating the catalytic promiscuity of P450 enzymes for multiple functional oxidations.
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Affiliation(s)
- Fengjie Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihan Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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2
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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3
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Zhang F, Zeng T, Wu R. QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. J Chem Inf Model 2023; 63:5018-5034. [PMID: 37556841 DOI: 10.1021/acs.jcim.3c00779] [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] [Indexed: 08/11/2023]
Abstract
Natural products and their derivatives are widely used across various industries, particularly pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing and meeting the growing need for diverse natural products. Natural enzymes, on the other hand, often exhibit unsatisfactory catalytic characteristics and necessitate further enzyme engineering modifications. QM/MM, as a powerful and extensively used computational tool in the field of enzyme catalysis, has been increasingly applied in rational enzyme engineering over the past decade. In this review, we summarize recent advances in QM/MM computational investigation on enzyme catalysis and enzyme engineering for natural product biosynthesis. The challenges and perspectives for future QM/MM applications aided enzyme engineering in natural product biosynthesis will also be discussed.
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Affiliation(s)
- Fan Zhang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Tao Zeng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
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4
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Li M, Miao H, Li Y, Wang F, Xu J. Protein Engineering of an Artificial P450BM3 Peroxygenase System Enables Highly Selective O-Demethylation of Lignin Monomers. Molecules 2022; 27:molecules27103120. [PMID: 35630597 PMCID: PMC9143554 DOI: 10.3390/molecules27103120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
The O-demethylation of lignin monomers, which has drawn substantial attention recently, is critical for the formation of phenols from aromatic ethers. The P450BM3 peroxygenase system was recently found to enable the O-demethylation of different aromatic ethers with the assistance of dual-functional small molecules (DFSM), but these prepared mutants only have either moderate O-demethylation activity or moderate selectivity, which hinders their further application. In this study, we improve the system by introducing different amino acids into the active site of P450BM3, and these amino acids with different side chains impacted the catalytic ability of enzymes due to their differences in size, polarity, and hydrophobicity. Among the prepared mutants, the combination of V78A/F87A/T268I/A264G and Im-C6-Phe efficiently catalyzed the O-demethylation of guaiacol (TON = 839) with 100% selectivity. Compared with NADPH-dependent systems, we offer an economical and practical bioconversion avenue.
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Affiliation(s)
- Maosheng Li
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China;
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Hengmin Miao
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Yanqing Li
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
- Correspondence: ; Tel.: +86-13869828530
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5
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Di S, Fan S, Jiang F, Cong Z. A Unique P450 Peroxygenase System Facilitated by a Dual-Functional Small Molecule: Concept, Application, and Perspective. Antioxidants (Basel) 2022; 11:antiox11030529. [PMID: 35326179 PMCID: PMC8944620 DOI: 10.3390/antiox11030529] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Cytochrome P450 monooxygenases (P450s) are promising versatile oxidative biocatalysts. However, the practical use of P450s in vitro is limited by their dependence on the co-enzyme NAD(P)H and the complex electron transport system. Using H2O2 simplifies the catalytic cycle of P450s; however, most P450s are inactive in the presence of H2O2. By mimicking the molecular structure and catalytic mechanism of natural peroxygenases and peroxidases, an artificial P450 peroxygenase system has been designed with the assistance of a dual-functional small molecule (DFSM). DFSMs, such as N-(ω-imidazolyl fatty acyl)-l-amino acids, use an acyl amino acid as an anchoring group to bind the enzyme, and the imidazolyl group at the other end functions as a general acid-base catalyst in the activation of H2O2. In combination with protein engineering, the DFSM-facilitated P450 peroxygenase system has been used in various oxidation reactions of non-native substrates, such as alkene epoxidation, thioanisole sulfoxidation, and alkanes and aromatic hydroxylation, which showed unique activities and selectivity. Moreover, the DFSM-facilitated P450 peroxygenase system can switch to the peroxidase mode by mechanism-guided protein engineering. In this short review, the design, mechanism, evolution, application, and perspective of these novel non-natural P450 peroxygenases for the oxidation of non-native substrates are discussed.
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Affiliation(s)
- Siyu Di
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengxian Fan
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengjie Jiang
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.D.); (S.F.); (F.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-532-80662758
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6
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Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM. Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:934-943. [PMID: 34990125 DOI: 10.1021/acs.jafc.1c06110] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.
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Affiliation(s)
- Abraham Vidal-Limon
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - José E Aguilar-Toalá
- Departamento de Ciencias de la Alimentación, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Avenida de las Garzas 10, Colonia El Panteón, Lerma de Villada, Estado de México 52005, Mexico
| | - Andrea M Liceaga
- Protein Chemistry and Bioactive Peptides Laboratory. Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, United States
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7
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Valle-Altamirano RG, Baratto MC, Badillo-Ramírez I, Gasteazoro F, Pogni R, Saniger JM, Valderrama B. Identification of Fe( iii)–OH species as a catalytic intermediate in plant peroxidases at high H 2O 2 concentration. NEW J CHEM 2022. [DOI: 10.1039/d1nj04837f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The structure for compound III formed after exposure of plant heme peroxidases to excess H2O2 seems to be a hydroxylated form, providing new evidence for understanding the structural basis of the substrate-induced suicidal behavior of these enzymes.
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Affiliation(s)
- Rodolfo G. Valle-Altamirano
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Francisco Gasteazoro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Brenda Valderrama
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
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8
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Ma N, Fang W, Liu C, Qin X, Wang X, Jin L, Wang B, Cong Z. Switching an Artificial P450 Peroxygenase into Peroxidase via Mechanism-Guided Protein Engineering. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenhan Fang
- Department of Chemistry, Xiamen University, Xiamen, Fujian 361005, China
| | - Chuanfei Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiangquan Qin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Department of Chemistry, College of Science, Yanbian University, Yanji, Jilin 133002, China
| | - Xiling Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Longyi Jin
- Department of Chemistry, College of Science, Yanbian University, Yanji, Jilin 133002, China
| | - Binju Wang
- Department of Chemistry, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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9
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Armbruster J, Steinmassl M, Müller Bogotá CA, Berg G, Nidetzky B, Dennig A. P450 Jα : A New, Robust and α-Selective Fatty Acid Hydroxylase Displaying Unexpected 1-Alkene Formation. Chemistry 2020; 26:15910-15921. [PMID: 32449211 DOI: 10.1002/chem.201905511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 05/14/2020] [Indexed: 01/01/2023]
Abstract
Oxyfunctionalization of fatty acids (FAs) is a key step in the design of novel synthetic pathways for biobased/biodegradable polymers, surfactants and fuels. Here, we show the isolation and characterization of a robust FA α-hydroxylase (P450Jα ) which catalyses the selective conversion of a broad range of FAs (C6:0-C16:0) and oleic acid (C18:1) with H2 O2 as oxidant. Under optimized reaction conditions P450Jα yields α-hydroxy acids all with >95 % regioselectivity, high specific activity (up to 15.2 U mg-1 ) and efficient coupling of oxidant to product (up to 85 %). Lauric acid (C12:0) turned out to be an excellent substrate with respect to productivity (TON=394 min-1 ). On preparative scale, conversion of C12:0 reached 83 % (0.9 g L-1 ) when supplementing H2 O2 in fed-batch mode. Under similar conditions P450Jα allowed further the first biocatalytic α-hydroxylation of oleic acid (88 % conversion on 100 mL scale) at high selectivity and in good yields (1.1 g L-1 ; 79 % isolated yield). Unexpectedly, P450Jα displayed also 1-alkene formation from shorter chain FAs (≤C10:0) showing that oxidative decarboxylation is more widely distributed across this enzyme family than reported previously.
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Affiliation(s)
- Julia Armbruster
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
| | - Mathilde Steinmassl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
| | - Christina A Müller Bogotá
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.,Institute of Environmental Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
| | - Gabriele Berg
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.,Institute of Environmental Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria.,Institute of Environmental Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
| | - Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria.,Institute of Environmental Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
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10
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Current state and future perspectives of engineered and artificial peroxygenases for the oxyfunctionalization of organic molecules. Nat Catal 2020. [DOI: 10.1038/s41929-020-00507-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Zhang L, Manley OM, Ma D, Yin Y, Makris TM, Wang Q. Enhanced P450 fatty acid decarboxylase catalysis by glucose oxidase coupling and co-assembly for biofuel generation. BIORESOURCE TECHNOLOGY 2020; 311:123538. [PMID: 32485602 DOI: 10.1016/j.biortech.2020.123538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Cytochrome P450 OleT is a fatty acid decarboxylase that uses hydrogen peroxide (H2O2) to catalyze the production of terminal alkenes, which are industrially important chemicals with biofuel and synthetic applications. Despite its requirement for large turnover levels, high concentrations of H2O2 may cause heme group degradation, diminishing enzymatic activity and limiting broad application for synthesis. Here, we report an artificial enzyme cascade composed of glucose oxidase (GOx) and OleTSA from Staphylococcus aureus for efficient terminal alkene production. By adjusting the ratio of GOx to OleTSA, the GOx-based tandem catalysis shows significantly improved product yield compared to the H2O2 injection method. Moreover, the co-assembly of the GOx/OleTSA enzymes with a polymer, forming polymer-dual enzymes nanoparticles, displays improved activity compared to the free enzyme. This dual strategy provides a simple and efficient system to transform a naturally abundant feedstock to industrially important chemicals.
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Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Olivia M Manley
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Dumei Ma
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA; Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.
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12
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Jiang Y, Wang C, Ma N, Chen J, Liu C, Wang F, Xu J, Cong Z. Regioselective aromatic O-demethylation with an artificial P450BM3 peroxygenase system. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00241k] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly regioselective O-demethylation of aromatic ethers related to the bioconversion of lignin was achieved by the H2O2-dependent engineered P450BM3 enzymes with assistance of a dual-functional small molecule (DFSM) for the first time.
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Affiliation(s)
- Yihui Jiang
- Key Lab of Sustainable Development of Polar Fisheries
- Ministry of Agriculture and Rural Affairs
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
- Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology
- Qingdao 266071
| | - Chunlan Wang
- Key Lab of Sustainable Development of Polar Fisheries
- Ministry of Agriculture and Rural Affairs
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
- Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology
- Qingdao 266071
| | - Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences
- Qingdao
- China
- University of Chinese Academy of Sciences
| | - Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences
- Qingdao
- China
- University of Chinese Academy of Sciences
| | - Chuanfei Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences
- Qingdao
- China
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries
- Ministry of Agriculture and Rural Affairs
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
- Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology
- Qingdao 266071
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries
- Ministry of Agriculture and Rural Affairs
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
- Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology
- Qingdao 266071
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences
- Qingdao
- China
- University of Chinese Academy of Sciences
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13
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Crystal structure of bacterial CYP116B5 heme domain: New insights on class VII P450s structural flexibility and peroxygenase activity. Int J Biol Macromol 2019; 140:577-587. [PMID: 31430491 DOI: 10.1016/j.ijbiomac.2019.08.141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 11/22/2022]
Abstract
Class VII cytochromes P450 are self-sufficient enzymes carrying a phthalate family oxygenase-like reductase domain and a P450 domain fused in a single polypeptide chain. The biocatalytic applications of CYP116B members are limited by the need of the NADPH cofactor and the lack of crystal structures as a starting point for protein engineering. Nevertheless, we demonstrated that the heme domain of CYP116B5 can use hydrogen peroxide as electron donor bypassing the need of NADPH. Here, we report the crystal structure of CYP116B5 heme domain in complex with histidine at 2.6 Å of resolution. The structure reveals the typical P450 fold and a closed conformation with an active site cavity of 284 Å3 in volume, accommodating a histidine molecule forming a hydrogen bond with the water molecule present as 6th heme iron ligand. MD simulations in the absence of any ligand revealed the opening of a tunnel connecting the active site to the protein surface through the movement of F-, G- and H-helices. A structural alignment with bacterial cytochromes P450 allowed the identification of amino acids in the proximal heme site potentially involved in peroxygenase activity. The availability of the crystal structure provides the bases for the structure-guided design of new biocatalysts.
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14
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X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state. Arch Biochem Biophys 2019; 666:107-115. [PMID: 30940570 DOI: 10.1016/j.abb.2019.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/21/2019] [Accepted: 03/29/2019] [Indexed: 11/22/2022]
Abstract
Catalases are biotechnologically relevant enzymes because of their applications in food technology, bioremediation, and biomedicine. The dismutation of hydrogen peroxide occurs in two steps; in the first one, the enzyme forms an oxidized compound I (Cpd I) and in the second one, the enzyme is reduced to the ferric state. In this research work, we analyzed the reduction of Cpd I by X-ray radiation damage during diffraction experiments in crystals of CAT-3, a Large-Size Subunit Catalase (LSC) from Neurospora crassa. A Multi-Crystal Data collection Strategy was applied in order to obtain the Cpd I structure at a resolution of 2.2 Å; this intermediate was highly sensitive to X-ray and was easily reduced at very low deposited radiation dose, causing breakage of the Fe=O bond. The comparison of the structures showed reduced intermediates and also evidenced the differential sensitivity per monomer. The resting ferric state was reduced to the ferrous state, an intermediate without a previous report in LSC. The chemically obtained Cpd I and the X-ray reduced intermediates were identified by UV-visible microspectrometry coupled to data collection. The differential sensitivity and the formation of a ferrous state are discussed, emphasizing the importance of the correct interpretation in the oxidation state of the iron heme.
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15
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Dennig A, Blaschke F, Gandomkar S, Tassano E, Nidetzky B. Preparative Asymmetric Synthesis of Canonical and Non‐canonical α‐amino Acids Through Formal Enantioselective Biocatalytic Amination of Carboxylic Acids. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology (acib) Petersgasse 14 8010 Graz Austria
| | - Fabio Blaschke
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
| | - Somayyeh Gandomkar
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
| | - Erika Tassano
- Department of ChemistryUniversity of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of TechnologyNAWI Graz Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology (acib) Petersgasse 14 8010 Graz Austria
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16
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Ma N, Chen Z, Chen J, Chen J, Wang C, Zhou H, Yao L, Shoji O, Watanabe Y, Cong Z. Dual-Functional Small Molecules for Generating an Efficient Cytochrome P450BM3 Peroxygenase. Angew Chem Int Ed Engl 2018; 57:7628-7633. [PMID: 29481719 DOI: 10.1002/anie.201801592] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 12/21/2022]
Abstract
We report a unique strategy for the development of a H2 O2 -dependent cytochrome P450BM3 system, which catalyzes the monooxygenation of non-native substrates with the assistance of dual-functional small molecules (DFSMs), such as N-(ω-imidazolyl fatty acyl)-l-amino acids. The acyl amino acid group of DFSM is responsible for bounding to enzyme as an anchoring group, while the imidazolyl group plays the role of general acid-base catalyst in the activation of H2 O2 . This system affords the best peroxygenase activity for the epoxidation of styrene, sulfoxidation of thioanisole, and hydroxylation of ethylbenzene among those P450-H2 O2 system previously reported. This work provides the first example of the activation of the normally H2 O2 -inert P450s through the introduction of an exogenous small molecule. This approach improves the potential use of P450s in organic synthesis as it avoids the expensive consumption of the reduced nicotinamide cofactor NAD(P)H and its dependent electron transport system. This introduces a promising approach for exploiting enzyme activity and function based on direct chemical intervention in the catalytic process.
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Affiliation(s)
- Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhifeng Chen
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingfei Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Cong Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Haifeng Zhou
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
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17
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Ma N, Chen Z, Chen J, Chen J, Wang C, Zhou H, Yao L, Shoji O, Watanabe Y, Cong Z. Dual-Functional Small Molecules for Generating an Efficient Cytochrome P450BM3 Peroxygenase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong 266101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Zhifeng Chen
- Hubei Key Laboratory of Natural Products Research and Development; College of Biological and Pharmaceutical Sciences; China Three Gorges University; Yichang Hubei 443002 China
| | - Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong 266101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jingfei Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong 266101 China
| | - Cong Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong 266101 China
| | - Haifeng Zhou
- Hubei Key Laboratory of Natural Products Research and Development; College of Biological and Pharmaceutical Sciences; China Three Gorges University; Yichang Hubei 443002 China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong 266101 China
| | - Osami Shoji
- Department of Chemistry; Graduate School of Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Yoshihito Watanabe
- Department of Chemistry; Graduate School of Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong 266101 China
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18
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Avelar M, Pastor N, Ramirez-Ramirez J, Ayala M. Replacement of oxidizable residues predicted by QM-MM simulation of a fungal laccase generates variants with higher operational stability. J Inorg Biochem 2018; 178:125-133. [DOI: 10.1016/j.jinorgbio.2017.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 11/28/2022]
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19
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20
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Dennig A, Weingartner AM, Kardashliev T, Müller CA, Tassano E, Schürmann M, Ruff AJ, Schwaneberg U. An Enzymatic Route to α-Tocopherol Synthons: Aromatic Hydroxylation of Pseudocumene and Mesitylene with P450 BM3. Chemistry 2017; 23:17981-17991. [PMID: 28990705 DOI: 10.1002/chem.201703647] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Indexed: 02/06/2023]
Abstract
Aromatic hydroxylation of pseudocumene (1 a) and mesitylene (1 b) with P450 BM3 yields key phenolic building blocks for α-tocopherol synthesis. The P450 BM3 wild-type (WT) catalyzed selective aromatic hydroxylation of 1 b (94 %), whereas 1 a was hydroxylated to a large extent on benzylic positions (46-64 %). Site-saturation mutagenesis generated a new P450 BM3 mutant, herein named "variant M3" (R47S, Y51W, A330F, I401M), with significantly increased coupling efficiency (3- to 8-fold) and activity (75- to 230-fold) for the conversion of 1 a and 1 b. Additional π-π interactions introduced by mutation A330F improved not only productivity and coupling efficiency, but also selectivity toward aromatic hydroxylation of 1 a (61 to 75 %). Under continuous nicotinamide adenine dinucleotide phosphate recycling, the novel P450 BM3 variant M3 was able to produce the key tocopherol precursor trimethylhydroquinone (3 a; 35 % selectivity; 0.18 mg mL-1 ) directly from 1 a. In the case of 1 b, overoxidation leads to dearomatization and the formation of a valuable p-quinol synthon that can directly serve as an educt for the synthesis of 3 a. Detailed product pattern analysis, substrate docking, and mechanistic considerations support the hypothesis that 1 a binds in an inverted orientation in the active site of P450 BM3 WT, relative to P450 BM3 variant M3, to allow this change in chemoselectivity. This study provides an enzymatic route to key phenolic synthons for α-tocopherols and the first catalytic and mechanistic insights into direct aromatic hydroxylation and dearomatization of trimethylbenzenes with O2 .
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Affiliation(s)
- Alexander Dennig
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | | | - Tsvetan Kardashliev
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | | | - Erika Tassano
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Martin Schürmann
- DSM Ahead R&D BV/DSM Innovative Synthesis, Post address: P.O. Box 1066, 6160 BB, Geleen, The Netherlands
| | - Anna Joëlle Ruff
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.,DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52074, Aachen, Germany
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21
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Enzymatic Activation of the Emerging Drug Resveratrol. Appl Biochem Biotechnol 2017; 185:248-256. [PMID: 29124656 DOI: 10.1007/s12010-017-2645-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
The plant originated stilbene "resveratrol" (3,4',5-trans-trihydroxystilbene) is well known for its diverse health benefits including anti-tumor, anti-inflammatory, anti-microbial, and anti-oxidant properties. Besides a significant amount of reports on different aspects of its application as prodrug in the last 50 years, still, a strategy leading to the production of the active drug is missing. The aim of this work was to evaluate the enzymatic activation of prodrug resveratrol to the effective drug piceatannol, without engaging expensive cofactors. Five different heme proteins were analyzed for the transformation of resveratrol. Kinetic parameters of resveratrol transformation and analysis of the transformed products were conducted through HPLC and GC-MS. Effect of pH and organic solvent on the transformation process had also been evaluated. Among all tested heme proteins, only a variant of cytochrome P450BM3 from Bacillus megaterium (CYPBM3F87A) was found suitable for piceatannol production. The most suitable pH for the reaction conditions was 8.5, while organic solvents did not show any effect on transformation. For resveratrol transformation, the turnover rate (k cat) was 21.7 (± 0.6) min-1, the affinity constant (K M) showed a value of 55.7 (± 16.7) μM for a catalytic efficiency (k cat/K M) of 389 min-1 mM-1. GC-MS analysis showed that the only product from resveratrol transformation by cytochrome P450BM3 is the biologically active piceatannol. The enzymatic transformation of resveratrol, an emerging compound with medical interest, to active product piceatannol by a variant of cytochrome P450BM3 in the absence of expensive NADPH cofactor is demonstrated. This enzymatic process is economically attractive and can be scaled up to cover the increasing medical demand for piceatannol.
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22
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Garcia-Borràs M, Houk KN, Jiménez-Osés G. Computational Design of Protein Function. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The computational design of enzymes is a tremendous challenge for both chemistry and biochemistry. The ability to design stable and functional biocatalysts that could operate under different conditions to perform chemical reactions without precedent in nature, allowing the large-scale production of chemicals à la carte, would revolutionise both synthetic, pharmacologic and materials chemistry. Despite the great advances achieved, this highly multidisciplinary area of research is still in its infancy. This chapter describes the ‘inside-out’ protocol for computational enzyme design and both the achievements and limitations of the current technology are highlighted. Furthermore, molecular dynamics simulations have proved to be invaluable in the enzyme design process, constituting an important tool for discovering elusive catalytically relevant conformations of the engineered or designed enzyme. As a complement to the ‘inside-out’ design protocol, different examples where hybrid QM/MM approaches have been directly applied to discover beneficial mutations in rational computational enzyme design are described.
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Affiliation(s)
- Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California Los Angeles California CA 90095-1569 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles California CA 90095-1569 USA
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
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23
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Belsare KD, Horn T, Ruff AJ, Martinez R, Magnusson A, Holtmann D, Schrader J, Schwaneberg U. Directed evolution of P450cin for mediated electron transfer. Protein Eng Des Sel 2016; 30:119-127. [PMID: 28007937 DOI: 10.1093/protein/gzw072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 11/28/2016] [Accepted: 12/05/2016] [Indexed: 11/13/2022] Open
Abstract
Directed evolution is a powerful method to optimize enzyme properties for application demands. Interesting targets are P450 monooxygenases which catalyze the stereo- and regiospecific hydroxylation of chemically inert C-H bonds. Synthesis employing P450s under cell-free reaction conditions is limited by low total turnover numbers, enzyme instability, low product yields and the requirement of the expensive co-factor NADPH. Bioelectrocatalysis is an alternative to replace NADPH in cell-free P450-catalyzed reactions. However, natural enzymes are often not suitable for using non-natural electron delivery systems. Here we report the directed evolution of a previously engineered P450 CinA-10aa-CinC fusion protein (named P450cin-ADD-CinC) to use zinc/cobalt(III)sepulchrate as electron delivery system for an increased hydroxylation activity of 1,8-cineole. Two rounds of Sequence Saturation Mutagenesis (SeSaM) each followed by one round of multiple site-saturation mutagenesis of the P450 CinA-10aa-CinC fusion protein generated a variant (Gln385His, Val386Ser, Thr77Asn, Leu88Arg; named KB8) with a 3.8-fold increase in catalytic efficiency (28 µM-1 min-1) compared to P450cin-ADD-CinC (7 µM-1 min-1). Furthermore, variant KB8 exhibited a 1.5-fold higher product formation (500 µM µM-1 P450) compared to the equimolar mixture of CinA, CinC and Fpr using NADPH as co-factor (315 µM µM-1 P450). In addition, electrochemical experiments with the electron delivery system platinum/cobalt(III)sepulchrate showed that the KB8 variant had a 4-fold higher product formation rate (0.16 nmol (nmol) P450-1 min-1 cm-2) than the P450cin-ADD-CinC (0.04 nmol (nmol) P450-1 min-1 cm-2). In summary, the current work shows prospects of using directed evolution to generate P450 enzymes suitable for use with alternative electron delivery systems.
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Affiliation(s)
- Ketaki D Belsare
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Thomas Horn
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ronny Martinez
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anders Magnusson
- Biochemical Engineering Group, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Dirk Holtmann
- Biochemical Engineering Group, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Jens Schrader
- Biochemical Engineering Group, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany .,DWI-Leibniz-Institut für Interaktive Materialien e. V., Forckenbeckstraße 50, 52074 Aachen, Germany
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24
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Exploring the catalase activity of unspecific peroxygenases and the mechanism of peroxide-dependent heme destruction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Quester K, Juarez-Moreno K, Secundino I, Roseinstein Y, Alejo KP, Huerta-Saquero A, Vazquez-Duhalt R. Cytochrome P450 Bioconjugate as a Nanovehicle for Improved Chemotherapy Treatment. Macromol Biosci 2016; 17. [DOI: 10.1002/mabi.201600374] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 10/20/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Katrin Quester
- Centro de Nanociencias y Nanotecnología; Universidad Nacional Autónoma de México; Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22760 Mexico
| | - Karla Juarez-Moreno
- Centro de Nanociencias y Nanotecnología; Universidad Nacional Autónoma de México; Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22760 Mexico
- CONACYT Research Fellow at Centro de Nanociencias y Nanotecnología; UNAM; Ensenada Baja California 22760 Mexico
| | - Isamel Secundino
- Instituto de Biotecnología; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Yvonne Roseinstein
- Instituto de Biotecnología; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Karla P. Alejo
- Centro de Nanociencias y Nanotecnología; Universidad Nacional Autónoma de México; Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22760 Mexico
| | - Alejandro Huerta-Saquero
- Centro de Nanociencias y Nanotecnología; Universidad Nacional Autónoma de México; Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22760 Mexico
| | - Rafael Vazquez-Duhalt
- Centro de Nanociencias y Nanotecnología; Universidad Nacional Autónoma de México; Km 107 carretera Tijuana-Ensenada Ensenada Baja California 22760 Mexico
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26
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Electron flow through biological molecules: does hole hopping protect proteins from oxidative damage? Q Rev Biophys 2016; 48:411-20. [PMID: 26537399 DOI: 10.1017/s0033583515000062] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Biological electron transfers often occur between metal-containing cofactors that are separated by very large molecular distances. Employing photosensitizer-modified iron and copper proteins, we have shown that single-step electron tunneling can occur on nanosecond to microsecond timescales at distances between 15 and 20 Å. We also have shown that charge transport can occur over even longer distances by hole hopping (multistep tunneling) through intervening tyrosines and tryptophans. In this perspective, we advance the hypothesis that such hole hopping through Tyr/Trp chains could protect oxygenase, dioxygenase, and peroxidase enzymes from oxidative damage. In support of this view, by examining the structures of P450 (CYP102A) and 2OG-Fe (TauD) enzymes, we have identified candidate Tyr/Trp chains that could transfer holes from uncoupled high-potential intermediates to reductants in contact with protein surface sites.
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27
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Gricman Ł, Weissenborn MJ, Hoffmann SM, Borlinghaus N, Hauer B, Pleiss J. Redox Partner Interaction Sites in Cytochrome P450 Monooxygenases:In SilicoAnalysis and Experimental Validation. ChemistrySelect 2016. [DOI: 10.1002/slct.201600369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sara M. Hoffmann
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Niels Borlinghaus
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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28
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Sánchez-Alejandro F, Juarez-Moreno K, Baratto MC, Basosi R, Vazquez-Duhalt R. Tryptophan-surface modification of versatile peroxidase from Bjerkandera adusta enhances its catalytic performance. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Galende PP, Cuadrado NH, Kostetsky EY, Roig MG, Kennedy JF, Shnyrov VL. Mechanism-based suicide inactivation of white Spanish broom (Cytisus multiflorus) peroxidase by excess hydrogen peroxide. Int J Biol Macromol 2015; 81:975-9. [DOI: 10.1016/j.ijbiomac.2015.09.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 12/01/2022]
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30
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Antioxidant Capacity of Poly(Ethylene Glycol) (PEG) as Protection Mechanism Against Hydrogen Peroxide Inactivation of Peroxidases. Appl Biochem Biotechnol 2015; 177:1364-73. [DOI: 10.1007/s12010-015-1820-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
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Dennig A, Kuhn M, Tassoti S, Thiessenhusen A, Gilch S, Bülter T, Haas T, Hall M, Faber K. Oxidative Decarboxylation of Short-Chain Fatty Acids to 1-Alkenes. Angew Chem Int Ed Engl 2015; 54:8819-22. [PMID: 26095212 DOI: 10.1002/anie.201502925] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 01/11/2023]
Abstract
The enzymatic oxidative decarboxylation of linear short-chain fatty acids (C4:0-C9:0) employing the P450 monooxygenase OleT, O2 as the oxidant, and NAD(P)H as the electron donor gave the corresponding terminal C3 to C8 alkenes with product titers of up to 0.93 g L(-1) and TTNs of >2000. Key to this process was the construction of an efficient electron-transfer chain employing putidaredoxin CamAB in combination with NAD(P)H recycling at the expense of glucose, formate, or phosphite. This system allows for the biocatalytic production of industrially important 1-alkenes, such as propene and 1-octene, from renewable resources for the first time.
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Affiliation(s)
- Alexander Dennig
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Miriam Kuhn
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Sebastian Tassoti
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Anja Thiessenhusen
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Stefan Gilch
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Thomas Bülter
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Thomas Haas
- Creavis, Evonik Industries, Bau 1420, Paul Baumann Strasse 1, 45772 Marl (Germany)
| | - Mélanie Hall
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria)
| | - Kurt Faber
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria).
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Dennig A, Kuhn M, Tassoti S, Thiessenhusen A, Gilch S, Bülter T, Haas T, Hall M, Faber K. Oxidative Decarboxylierung von kurzkettigen Fettsäuren zu 1-Alkenen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502925] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hlavica P. Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:247-97. [PMID: 26002739 DOI: 10.1007/978-3-319-16009-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie der LMU, Goethestrasse 33, 80336, München, Germany,
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Chemotherapy pro-drug activation by biocatalytic virus-like nanoparticles containing cytochrome P450. Enzyme Microb Technol 2014; 60:24-31. [PMID: 24835096 DOI: 10.1016/j.enzmictec.2014.04.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/11/2014] [Accepted: 04/02/2014] [Indexed: 11/22/2022]
Abstract
This work shows, for the first time, the encapsulation of a highly relevant protein in the biomedical field into virus-like particles (VLPs). A bacterial CYP variant was effectively encapsulated in VLPs constituted of coat protein from cowpea chlorotic mottle virus (CCMV). The catalytic VLPs are able to transform the chemotherapeutic pro-drug, tamoxifen, and the emerging pro-drug resveratrol. The chemical nature of the products was identified, confirming similar active products than those obtained with human CYP. The enzymatic VLPs remain stable after the catalytic reaction. The potential use of these biocatalytic nanoparticles as targeted CYP carriers for the activation of chemotherapy drugs is discussed.
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Shoji O, Watanabe Y. Peroxygenase reactions catalyzed by cytochromes P450. J Biol Inorg Chem 2014; 19:529-39. [DOI: 10.1007/s00775-014-1106-9] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022]
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Vazquez-Duhalt R, Aguila SA, Arrocha AA, Ayala M. QM/MM Molecular Modeling and Marcus Theory in the Molecular Design of Electrodes for Enzymatic Fuel Cells. ChemElectroChem 2013. [DOI: 10.1002/celc.201300096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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