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Miller AH, Martins IBS, Blagova EV, Wilson KS, Duhme-Klair AK. Kinetic and structural analysis of redox-reversible artificial imine reductases. J Inorg Biochem 2024; 260:112691. [PMID: 39126757 DOI: 10.1016/j.jinorgbio.2024.112691] [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: 06/10/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Three artificial imine reductases, constructed via supramolecular anchoring utilising FeIII-azotochelin, a natural siderophore, to bind an iridium-containing catalyst to periplasmic siderophore-binding protein (PBP) scaffolds, have previously been synthesised and subjected to catalytic testing. Despite exhibiting high homology and possessing conserved siderophore anchor coordinating residues, the three artificial metalloenzymes (ArMs) displayed significant variability in turnover frequencies (TOFs). To further understand the catalytic properties of these ArMs, their kinetic behaviour was evaluated with respect to the reduction of three cyclic imines: dihydroisoquinoline, harmaline, and papaverine. Kinetic analyses revealed that all examined ArMs adhere to Michaelis-Menten kinetics, with the most pronounced saturation profile observed for the substrate harmaline. Additionally, molecular docking studies suggested varied hydrogen-bonding interactions between substrates and residues within the artificial binding pocket. Pi-stacking and pi-cation interactions were identified for harmaline and papaverine, corroborating the higher affinity of these substrates for the ArMs in comparison to dihydroisoquinoline. Furthermore, it was demonstrated that multiple cavities are capable of accommodating substrates in close proximity to the catalytic centre, thereby rationalising the moderate enantioselectivity conferred by the unmodified scaffolds.
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Affiliation(s)
- Alex H Miller
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Ingrid B S Martins
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Elena V Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Keith S Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Anne-K Duhme-Klair
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom.
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Huang W, Wan Y, Su H, Zhang Z, Liu Y, Sadeeq M, Xian M, Feng X, Xiong P, Hou F. Recent Advances in Phenazine Natural Products: Biosynthesis and Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21364-21379. [PMID: 39300971 DOI: 10.1021/acs.jafc.4c05294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Phenazine natural products are a class of nitrogen-containing heterocyclic compounds produced by microorganisms. The tricyclic ring molecules show various chemical structures and extensive pharmacological activities, such as antimicrobial, anticancer, antiparasitic, anti-inflammatory, and insecticidal activities, with low toxicity to the environment. Since phenazine-1-carboxylic acid has been developed as a registered biopesticide, the application of phenazine natural products will be promising in the field of agriculture pathogenic fungi control based on broad-spectrum antifungal activity, minimal toxicity to the environment, and improvement of crop production. Currently, there are still plenty of intriguing hidden biosynthetic pathways of phenazine natural products to be discovered, and the titer of naturally occurring phenazine natural products is insufficient for agricultural applications. In this review, we spotlight the progress regarding biosynthesis and metabolic engineering research of phenazine natural products in the past decade. The review provides useful insights concerning phenazine natural products production and more clues on new phenazine derivatives biosynthesis.
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Affiliation(s)
- Wei Huang
- Shandong Freda Biotech Co., Ltd, 250101 Jinan, China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Yupeng Wan
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Huai Su
- Shandong Freda Biotech Co., Ltd, 250101 Jinan, China
| | - Zhe Zhang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Yingjie Liu
- Shandong Freda Biotech Co., Ltd, 250101 Jinan, China
| | - Mohd Sadeeq
- Shandong University of Technology, School of Life Sciences and Medicine, 255000 Zibo, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Peng Xiong
- Shandong University of Technology, School of Life Sciences and Medicine, 255000 Zibo, China
| | - Feifei Hou
- Shandong University of Technology, School of Life Sciences and Medicine, 255000 Zibo, China
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Lin YW. Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions. J Inorg Biochem 2024; 257:112595. [PMID: 38759262 DOI: 10.1016/j.jinorgbio.2024.112595] [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: 03/25/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China.
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Chen ZY, Yuan H, Wang H, Sun LJ, Yu L, Gao SQ, Tan X, Lin YW. Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin. Chembiochem 2024; 25:e202300678. [PMID: 38015421 DOI: 10.1002/cbic.202300678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 11/29/2023]
Abstract
Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.
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Affiliation(s)
- Ze-Yuan Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Huamin Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
- Hengyang Medical School, University of South China, Hengyang, 421001, China
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Tang S, Sun LJ, Pan AQ, Huang J, Wang H, Lin YW. Application of engineered myoglobins for biosynthesis of clofazimine by integration with chemical synthesis. Org Biomol Chem 2023; 21:9603-9609. [PMID: 38014756 DOI: 10.1039/d3ob01687k] [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: 11/29/2023]
Abstract
Significant efforts have been made in the design of artificial metalloenzymes. Myoglobin (Mb), an O2 carrier, has been engineered to exhibit different functions. Herein, we applied a series of engineered Mb mutants with peroxidase activity for biosynthesis of clofazimine (CFZ), a potential drug with a broad-spectrum antiviral activity, by integration with chemical synthesis. Two of those mutants, F43Y Mb and F43Y/T67R Mb, have been shown to efficiently catalyze the oxidative coupling of 2-N-(4-chlorophenyl) benzene-1,2-diamine (N-4-CPBDA) in the presence of H2O2, with 97% yields. The overall catalytic efficiency (kcat/Km) is 46-fold and 82-fold higher than that of WT Mb, respectively. By further combination of this reaction with chemical synthesis, the production of CFZ was accomplished with an isolated yield of 72%. These results showed that engineered Mbs containing the Tyr-heme cross-link (F43Y Mb and F43Y/T67R Mb) exhibit enhanced activity in the oxidative coupling reaction. This study also indicates that the combination of biocatalysis and chemical synthesis avoids the need for the separation of intermediate products, which offers a convenient approach for the total synthesis of the biological compound CFZ.
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Affiliation(s)
- Shuai Tang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Li-Juan Sun
- Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Ai-Qun Pan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Jun Huang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Huamin Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
- Hengyang Medical College, University of South China, Hengyang 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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Sun LJ, Yuan H, Yu L, Gao SQ, Wen GB, Tan X, Lin YW. Structural and functional regulations by a disulfide bond designed in myoglobin like human neuroglobin. Chem Commun (Camb) 2022; 58:5885-5888. [PMID: 35471205 DOI: 10.1039/d2cc01753a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An artificial disulfide bond (Cys46-Cys61) was designed in the heme distal site of myoglobin, which regulates the conformation of the heme distal His64 and the protein reactivity, as confirmed by X-ray crystallography, EPR, and kinetic UV-vis studies. This study shows the successful design of a disulfide bond with suitable positions in globins, conferring a structure and function like those of the native human neuroglobin.
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Affiliation(s)
- Li-Juan Sun
- Hengyang Medical College, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Shu-Qin Gao
- Hengyang Medical College, University of South China, Hengyang 421001, China. .,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Hengyang Medical College, University of South China, Hengyang 421001, China. .,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- Hengyang Medical College, University of South China, Hengyang 421001, China. .,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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Gao SQ, Yuan H, Yang XZ, Xiang HF, Tan X, Wen GB, Lin YW. Improving the cell-membrane-penetrating activity of globins by introducing positive charges on protein surface: A case study of sperm whale myoglobin. Biochem Biophys Res Commun 2022; 598:26-31. [PMID: 35151200 DOI: 10.1016/j.bbrc.2022.02.013] [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: 01/17/2022] [Accepted: 02/05/2022] [Indexed: 11/18/2022]
Abstract
Globins are heme proteins such as hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb), playing important roles in biological system. In addition to normal functions, zebrafish Ngb was able to penetrate cell membranes, whereas less was known for other globin members. In this study, to improve the cell-membrane-penetrating activity of globins, we used sperm whale Mb as a model protein and constructed a quadruple mutant of G5K/Q8K/A19K/V21K Mb (termed 4K Mb), by introduction of four positive charges on the protein surface, which was designed according to the amino acid alignment with that of zebrafish Ngb. Spectroscopic and crystallographic studies showed that the four positively charged Lys residues did not affect the protein structure. Cell-membrane-penetrating essay further showed that 4K Mb exhibited enhanced activity compared to that of native Mb. This study provides valuable information for the effect of distribution of charged residues on the protein structure and the cell-membrane-penetrating activity of globins. Therefore, it will guide the design of protein-based biomaterials for biological applications.
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Affiliation(s)
- Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Xin-Zhi Yang
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Heng-Fang Xiang
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ge-Bo Wen
- Hengyang Medical School, University of South China, Hengyang, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China.
| | - Ying-Wu Lin
- Hengyang Medical School, University of South China, Hengyang, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China.
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Guo WJ, Xu JK, Wu ST, Gao SQ, Wen GB, Tan X, Lin YW. Design and Engineering of an Efficient Peroxidase Using Myoglobin for Dye Decolorization and Lignin Bioconversion. Int J Mol Sci 2021; 23:ijms23010413. [PMID: 35008837 PMCID: PMC8745427 DOI: 10.3390/ijms23010413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
The treatment of environmental pollutants such as synthetic dyes and lignin has received much attention, especially for biotechnological treatments using both native and artificial metalloenzymes. In this study, we designed and engineered an efficient peroxidase using the O2 carrier myoglobin (Mb) as a protein scaffold by four mutations (F43Y/T67R/P88W/F138W), which combines the key structural features of natural peroxidases such as the presence of a conserved His-Arg pair and Tyr/Trp residues close to the heme active center. Kinetic studies revealed that the quadruple mutant exhibits considerably enhanced peroxidase activity, with the catalytic efficiency (kcat/Km) comparable to that of the most efficient natural enzyme, horseradish peroxidase (HRP). Moreover, the designed enzyme can effectively decolorize a variety of synthetic organic dyes and catalyze the bioconversion of lignin, such as Kraft lignin and a model compound, guaiacylglycerol-β-guaiacyl ether (GGE). As analyzed by HPLC and ESI-MS, we identified several bioconversion products of GGE, as produced via bond cleavage followed by dimerization or trimerization, which illustrates the mechanism for lignin bioconversion. This study indicates that the designed enzyme could be exploited for the decolorization of textile wastewater contaminated with various dyes, as well as for the bioconversion of lignin to produce more value-added products.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
| | - Jia-Kun Xu
- Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China;
| | - Sheng-Tao Wu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
| | - Shu-Qin Gao
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
| | - Ge-Bo Wen
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China;
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
- Correspondence: ; Tel.: +86-734-8282375
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