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de O G Silva C, Sun P, Barrett K, Sanders MG, van Berkel WJH, Kabel MA, Meyer AS, Agger JW. Polyphenol Oxidase Activity on Guaiacyl and Syringyl Lignin Units. Angew Chem Int Ed Engl 2024; 63:e202409324. [PMID: 39285758 DOI: 10.1002/anie.202409324] [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: 05/16/2024] [Indexed: 11/01/2024]
Abstract
The natural heterogeneity of guaiacyl (G) and syringyl (S) compounds resulting from lignin processing hampers their direct use as plant-based chemicals and materials. Herein, we explore six short polyphenol oxidases (PPOs) from lignocellulose-degrading ascomycetes for their capacity to react with G-type and S-type phenolic compounds. All six PPOs catalyze the ortho-hydroxylation of G-type compounds (guaiacol, vanillic acid, and ferulic acid), forming the corresponding methoxy-ortho-diphenols. Remarkably, a subset of these PPOs is also active towards S-compounds (syringol, syringic acid, and sinapic acid) resulting in identical methoxy-ortho-diphenols. Assays with 18O2 demonstrate that these PPOs in particular catalyze ortho-hydroxylation and ortho-demethoxylation of S-compounds and generate methanol as a co-product. Oxidative (ortho-) demethoxylation of S-compounds is a novel reaction for PPOs, which we propose occurs by a distinct reaction mechanism as compared to aryl-O-demethylases. We further show that addition of a reducing agent can steer the PPO reaction to form methoxy-ortho-diphenols from both G- and S-type substrates rather than reactive quinones that lead to unfavorable polymerization. Application of PPOs opens for new routes to reduce the heterogeneity and methoxylation degree of mixtures of G and S lignin-derived compounds.
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Affiliation(s)
- Caio de O G Silva
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, Kgs., Lyngby, 2800, Denmark
| | - Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The, Netherlands
| | - Kristian Barrett
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, Kgs., Lyngby, 2800, Denmark
| | - Mark G Sanders
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The, Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The, Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The, Netherlands
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, Kgs., Lyngby, 2800, Denmark
| | - Jane W Agger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, Kgs., Lyngby, 2800, Denmark
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2
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Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
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Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
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Huang Y, Gao C, Song W, Wei W, Chen X, Gao C, Liu J, Wu J, Liu L. Improving Theaflavin-3,3'-digallate Production Efficiency Optimization by Transition State Conformation of Polyphenol Oxidase. Molecules 2023; 28:molecules28093831. [PMID: 37175239 PMCID: PMC10179947 DOI: 10.3390/molecules28093831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Theaflavins (TFs) are good for health because of their bioactivities. Enzymatic synthesis of TFs has garnered much attention; however, the source and activity of the enzymes needed limit their wide application. In this study, a microbial polyphenol oxidase from Bacillus megaterium was screened for the synthesis of theaflavin-3,3'-digallate (TFDG). Based on structural and mechanistic analyses of the enzyme, the O-O bond dissociation was identified as the rate-determining step. To address this issue, a transition state (TS) conformation optimization strategy was adopted to stabilize the spatial conformation of the O-O bond dissociation, which improved the catalytic efficiency of tyrosinase. Under the optimum transformation conditions of pH 4.0, temperature 25 °C, (-)-epigallocatechin gallate/epicatechin gallate molar ratio of 2:1, and time of 30 min, Mu4 (BmTyrV218A/R209S) produced 960.36 mg/L TFDG with a 44.22% conversion rate, which was 6.35-fold higher than that of the wild type. Thus, the method established has great potential in the synthesis of TFDG and other TFs.
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Affiliation(s)
- Ying Huang
- School of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Changzheng Gao
- Department of Cardiology, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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Kulandaivel S, Lin CH, Yeh YC. A bioinspired copper-based coordination polymer for the detection of pheochromocytoma biomarkers. Talanta 2023; 255:124206. [PMID: 36563506 DOI: 10.1016/j.talanta.2022.124206] [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: 09/23/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
Oxidase-mimicking (catechol oxidase/laccase) nanozymes provide outstanding specificity in the detection of epinephrine (Epi) for the assessment of pheochromocytoma; however, epinephrine (Epi) and norepinephrine (NE) co-existing in the same systems will reduce the selectivity of the biosensor. In the current study, we synthesized copper-based coordination polymer (Cu-CP) nanozymes capable of accelerating the oxidation of Epi with high specificity. Furthermore, the Cu-CP is able to detect Epi over a wide linear range of 0.5-100 μM with a low detection limit of 0.36 μM while providing excellent stability and recyclability. Furthermore, we employed colorimetric and fluorescence signals for sequential detection of the coexistence of Epi and NE for use in tracking the treatment outcomes of patients with pheochromocytoma. Experiments using artificial urine further confirmed the efficacy of the proposed system.
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Affiliation(s)
| | - Chia-Her Lin
- Department of Chemistry, National Taiwan Normal University, Taipei, 116, Taiwan.
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei, 116, Taiwan.
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Kipouros I, Stańczak A, Ginsbach JW, Andrikopoulos PC, Rulíšek L, Solomon EI. Elucidation of the tyrosinase/O 2/monophenol ternary intermediate that dictates the monooxygenation mechanism in melanin biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2205619119. [PMID: 35939688 PMCID: PMC9389030 DOI: 10.1073/pnas.2205619119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Melanins are highly conjugated biopolymer pigments that provide photoprotection in a wide array of organisms, from bacteria to humans. The rate-limiting step in melanin biosynthesis, which is the ortho-hydroxylation of the amino acid L-tyrosine to L-DOPA, is catalyzed by the ubiquitous enzyme tyrosinase (Ty). Ty contains a coupled binuclear copper active site that binds O2 to form a μ:η2:η2-peroxide dicopper(II) intermediate (oxy-Ty), capable of performing the regioselective monooxygenation of para-substituted monophenols to catechols. The mechanism of this critical monooxygenation reaction remains poorly understood despite extensive efforts. In this study, we have employed a combination of spectroscopic, kinetic, and computational methods to trap and characterize the elusive catalytic ternary intermediate (Ty/O2/monophenol) under single-turnover conditions and obtain molecular-level mechanistic insights into its monooxygenation reactivity. Our experimental results, coupled with quantum-mechanics/molecular-mechanics calculations, reveal that the monophenol substrate docks in the active-site pocket of oxy-Ty fully protonated, without coordination to a copper or cleavage of the μ:η2:η2-peroxide O-O bond. Formation of this ternary intermediate involves the displacement of active-site water molecules by the substrate and replacement of their H bonds to the μ:η2:η2-peroxide by a single H bond from the substrate hydroxyl group. This H-bonding interaction in the ternary intermediate enables the unprecedented monooxygenation mechanism, where the μ-η2:η2-peroxide O-O bond is cleaved to accept the phenolic proton, followed by substrate phenolate coordination to a copper site concomitant with its aromatic ortho-hydroxylation by the nonprotonated μ-oxo. This study provides insights into O2 activation and reactivity by coupled binuclear copper active sites with fundamental implications in biocatalysis.
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Affiliation(s)
- Ioannis Kipouros
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Agnieszka Stańczak
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague 6, Czech Republic
- Faculty of Science, Charles University, 128 00 Prague 2, Czech Republic
| | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Prokopis C. Andrikopoulos
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague 6, Czech Republic
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
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