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Tan W, Li X, Zhang P, Yao X, Li J, Jin P, Li K. A fatty acid photodecarboxylase-mimicking photonanozyme with defect-induced enzymatic substrate-binding pockets. J Colloid Interface Sci 2023; 652:1965-1973. [PMID: 37690304 DOI: 10.1016/j.jcis.2023.09.020] [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: 06/12/2023] [Revised: 08/20/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Hydrocarbon synthesis hints at the significance of in-depth investigations and detailed explanations of mimicking fatty acid photodecarboxylase (FAP). Considering the importance of photodecarboxylases in hydrocarbon synthesis, we present the potential of defective semiconductor nanomaterials as a novel type of photonanozymes (PNZs) that mimic enzyme-like performance, serving as alternatives to FAP. Ferrum-doped titanium dioxide (Fe-TiO2) was synthesized to introduce appropriate amounts of surface defects including reduced Ti3+ sites and oxygen vacancies, which reduce the band gap of TiO2 and enhance the visible-light absorption, thereby facilitating efficient charge trapping. Notably, the surface defects of Fe-TiO2 PNZs singularly act as enzymatic substrate-binding pockets that enable efficient carboxylic acid adsorption during the dark process, conversely facilitating the formation of more defects and boosting the FAP-like activity for photocatalytic decarboxylation reactions. This work provides a creative strategy for designing substrate-dependent higher-concentration defects as enzyme-like binding sites on promising PNZs that mimic natural photoenzymes.
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Affiliation(s)
- Wenlong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Pei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Xuyan Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Jinzhao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Peng Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China.
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2
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Song L, Meng X, Zhao J, Han H, Zheng D. Excited-state intramolecular double proton transfer mechanism associated with solvent polarity for 9,9-dimethyl-3,6-dihydroxy-2,7-bis(4,5-dihydro-4,4-dimethyl-2-oxazolyl)fluorene compound. Mol Phys 2021. [DOI: 10.1080/00268976.2021.2007307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Liying Song
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
| | - Xuan Meng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
| | - Haiyun Han
- People's Hospital of Dingtao District, Heze, People’s Republic of China
| | - Daoyuan Zheng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
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3
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Zeng Y, Liu L, Chen B, Zhang W. Light-Driven Enzymatic Decarboxylation of Dicarboxylic Acids. ChemistryOpen 2021; 10:553-559. [PMID: 33945237 PMCID: PMC8095292 DOI: 10.1002/open.202100039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Indexed: 11/24/2022] Open
Abstract
Photodecarboxylase from Chlorella variabillis (CvFAP) is one of the three known light-activated enzymes that catalyzes the decarboxylation of fatty acids into the corresponding C1-shortened alkanes. Although the substrate scope of CvFAP has been altered by protein engineering and decoy molecules, it is still limited to mono-fatty acids. Our studies demonstrate for the first time that long chain dicarboxylic acids can be converted by CvFAP. Notably, the conversion of dicarboxylic acids to alkanes still represents a chemically very challenging reaction. Herein, the light-driven enzymatic decarboxylation of dicarboxylic acids to the corresponding (C2-shortened) alkanes using CvFAP is described. A series of dicarboxylic acids is decarboxylated into alkanes in good yields by means of this approach, even for the preparative scales. Reaction pathway studies show that mono-fatty acids are formed as the intermediate products before the final release of C2-shortened alkanes. In addition, the thermostability, storage stability, and recyclability of CvFAP for decarboxylation of dicarboxylic acids are well evaluated. These results represent an advancement over the current state-of-the-art.
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Affiliation(s)
- Yong‐Yi Zeng
- School of Marine SciencesSun Yat-Sen UniversityZhuhai519082P. R. China
| | - Lan Liu
- School of Marine SciencesSun Yat-Sen UniversityZhuhai519082P. R. China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519082P. R. China
| | - Bi‐Shuang Chen
- School of Marine SciencesSun Yat-Sen UniversityZhuhai519082P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal EngineeringZhuhai519082P. R. China
| | - Wuyuan Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th AvenueTianjin300308P. R. China
- National Technology Innovation Center of Synthetic Biology32 West 7th AvenueTianjin300308P. R. China
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4
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Poddar H, Heyes DJ, Schirò G, Weik M, Leys D, Scrutton NS. A guide to time-resolved structural analysis of light-activated proteins. FEBS J 2021; 289:576-595. [PMID: 33864718 DOI: 10.1111/febs.15880] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Light-activated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enables the desired chemical and/or biological output response. Time-resolved serial femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
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Huijbers MME, Zhang W, Tonin F, Hollmann F. Lichtgetriebene enzymatische Decarboxylierung von Fettsäuren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807119] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mieke M. E. Huijbers
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
| | - Wuyuan Zhang
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
| | - Fabio Tonin
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
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Huijbers MME, Zhang W, Tonin F, Hollmann F. Light-Driven Enzymatic Decarboxylation of Fatty Acids. Angew Chem Int Ed Engl 2018; 57:13648-13651. [PMID: 30106504 PMCID: PMC6197046 DOI: 10.1002/anie.201807119] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Indexed: 11/10/2022]
Abstract
The photoenzymatic decarboxylation of fatty acids to alkanes is proposed as an alternative approach for the synthesis of biodiesel. By using a recently discovered photodecarboxylase from Chlorella variabilis NC64A (CvFAP) we demonstrate the irreversible preparation of alkanes from fatty acids and triglycerides. Several fatty acids and their triglycerides are converted by CvFAP in near‐quantitative yield and exclusive selectivity upon illumination with blue light. Very promising turnover numbers of up to 8000 were achieved in this proof‐of‐concept study.
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Affiliation(s)
- Mieke M E Huijbers
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Wuyuan Zhang
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
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7
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Gholami S, Nenov A, Rivalta I, Bocola M, Bordbar AK, Schwaneberg U, Davari MD, Garavelli M. Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols. J Phys Chem B 2018; 122:7668-7681. [PMID: 29996651 DOI: 10.1021/acs.jpcb.8b04231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm-1 red shift of the C13(1) carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q x electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.
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Affiliation(s)
- Samira Gholami
- Department of Chemistry , University of Isfahan , Isfahan 81746-73441 , Iran.,Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Ivan Rivalta
- Université de Lyon , École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 , Lyon , France
| | - Marco Bocola
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , 52074 Aachen , Germany
| | - A Khalegh Bordbar
- Department of Chemistry , University of Isfahan , Isfahan 81746-73441 , Iran
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , 52074 Aachen , Germany.,DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Mehdi D Davari
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , 52074 Aachen , Germany
| | - Marco Garavelli
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
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Archipowa N, Kutta RJ, Heyes DJ, Scrutton NS. Stepwise Hydride Transfer in a Biological System: Insights into the Reaction Mechanism of the Light-Dependent Protochlorophyllide Oxidoreductase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nataliya Archipowa
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Roger J. Kutta
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
- Current address: Institut für Physikalische und Theoretische Chemie; Universität Regensburg; Universitätsstr. 31 93053 Regensburg Germany
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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9
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Archipowa N, Kutta RJ, Heyes DJ, Scrutton NS. Stepwise Hydride Transfer in a Biological System: Insights into the Reaction Mechanism of the Light-Dependent Protochlorophyllide Oxidoreductase. Angew Chem Int Ed Engl 2018; 57:2682-2686. [PMID: 29363234 PMCID: PMC5861667 DOI: 10.1002/anie.201712729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/22/2018] [Indexed: 11/24/2022]
Abstract
Hydride transfer plays a crucial role in a wide range of biological systems. However, its mode of action (concerted or stepwise) is still under debate. Light‐dependent NADPH: protochlorophyllide oxidoreductase (POR) catalyzes the stereospecific trans addition of a hydride anion and a proton across the C17−C18 double bond of protochlorophyllide. Time‐resolved absorption and emission spectroscopy were used to investigate the hydride transfer mechanism in POR. Apart from excited states of protochlorophyllide, three discrete intermediates were resolved, consistent with a stepwise mechanism that involves an initial electron transfer from NADPH. A subsequent proton‐coupled electron transfer followed by a proton transfer yield distinct different intermediates for wild type and the C226S variant, that is, initial hydride attaches to either C17 or C18, but ends in the same chlorophyllide stereoisomer. This work provides the first evidence of a stepwise hydride transfer in a biological system.
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Affiliation(s)
- Nataliya Archipowa
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Roger J Kutta
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Current address: Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Derren J Heyes
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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