1
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Souza PMP, Carballares D, Gonçalves LRB, Fernandez-Lafuente R, Rodrigues S. Immobilization of Lipase B from Candida antarctica in Octyl-Vinyl Sulfone Agarose: Effect of the Enzyme-Support Interactions on Enzyme Activity, Specificity, Structure and Inactivation Pathway. Int J Mol Sci 2022; 23:ijms232214268. [PMID: 36430745 PMCID: PMC9697615 DOI: 10.3390/ijms232214268] [Citation(s) in RCA: 2] [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: 10/06/2022] [Revised: 10/21/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Lipase B from Candida antarctica was immobilized on heterofunctional support octyl agarose activated with vinyl sulfone to prevent enzyme release under drastic conditions. Covalent attachment was established, but the blocking step using hexylamine, ethylenediamine or the amino acids glycine (Gly) and aspartic acid (Asp) altered the results. The activities were lower than those observed using the octyl biocatalyst, except when using ethylenediamine as blocking reagent and p-nitrophenol butyrate (pNPB) as substrate. The enzyme stability increased using these new biocatalysts at pH 7 and 9 using all blocking agents (much more significantly at pH 9), while it decreased at pH 5 except when using Gly as blocking agent. The stress inactivation of the biocatalysts decreased the enzyme activity versus three different substrates (pNPB, S-methyl mandelate and triacetin) in a relatively similar fashion. The tryptophane (Trp) fluorescence spectra were different for the biocatalysts, suggesting different enzyme conformations. However, the fluorescence spectra changes during the inactivation were not too different except for the biocatalyst blocked with Asp, suggesting that, except for this biocatalyst, the inactivation pathways may not be so different.
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Affiliation(s)
- Priscila M. P. Souza
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Food Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 858, Fortaleza CEP 60440-900, CE, Brazil
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | - Luciana R. B. Gonçalves
- Chemical Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 709, Fortaleza CEP 60440-900, CE, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Center of Excellence in Bionanoscience Research, Member of the External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (R.F.-L.); (S.R.)
| | - Sueli Rodrigues
- Food Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 858, Fortaleza CEP 60440-900, CE, Brazil
- Correspondence: (R.F.-L.); (S.R.)
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2
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Yu S, Li J, Yao P, Feng J, Cui Y, Li J, Liu X, Wu Q, Lin J, Zhu D. Inverting the Enantiopreference of Nitrilase‐Catalyzed Desymmetric Hydrolysis of Prochiral Dinitriles by Reshaping the Binding Pocket with a Mirror‐Image Strategy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shanshan Yu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jinlong Li
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Peiyuan Yao
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jinhui Feng
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Yunfeng Cui
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jianjiong Li
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Xiangtao Liu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Qiaqing Wu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jianping Lin
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Dunming Zhu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
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3
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Yu S, Li J, Yao P, Feng J, Cui Y, Li J, Liu X, Wu Q, Lin J, Zhu D. Inverting the Enantiopreference of Nitrilase‐Catalyzed Desymmetric Hydrolysis of Prochiral Dinitriles by Reshaping the Binding Pocket with a Mirror‐Image Strategy. Angew Chem Int Ed Engl 2020; 60:3679-3684. [DOI: 10.1002/anie.202012243] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/19/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Shanshan Yu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jinlong Li
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Peiyuan Yao
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jinhui Feng
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Yunfeng Cui
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jianjiong Li
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Xiangtao Liu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Qiaqing Wu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Jianping Lin
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Dunming Zhu
- National Technology Innovation Center of Synthetic Biology National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 P. R. China
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4
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Biler M, Crean RM, Schweiger AK, Kourist R, Kamerlin SCL. Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase. J Am Chem Soc 2020; 142:20216-20231. [PMID: 33180505 PMCID: PMC7735706 DOI: 10.1021/jacs.0c10701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity, and selectivity of this enzyme are only poorly understood to date, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the nonconverted or poorly converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering.
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Affiliation(s)
- Michal Biler
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Rory M. Crean
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Anna K. Schweiger
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
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5
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Enoki J, Mügge C, Tischler D, Miyamoto K, Kourist R. Chemoenzymatic Cascade Synthesis of Optically Pure Alkanoic Acids by Using Engineered Arylmalonate Decarboxylase Variants. Chemistry 2019; 25:5071-5076. [PMID: 30702787 PMCID: PMC6563808 DOI: 10.1002/chem.201806339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 11/09/2022]
Abstract
Arylmalonate decarboxylase (AMDase) catalyzes the cofactor‐free asymmetric decarboxylation of prochiral arylmalonic acids and produces the corresponding monoacids with rigorous R selectivity. Alteration of catalytic cysteine residues and of the hydrophobic environment in the active site by protein engineering has previously resulted in the generation of variants with opposite enantioselectivity and improved catalytic performance. The substrate spectrum of AMDase allows it to catalyze the asymmetric decarboxylation of small methylvinylmalonic acid derivatives, implying the possibility to produce short‐chain 2‐methylalkanoic acids with high optical purity after reduction of the nonactivated C=C double bond. Use of diimide as the reductant proved to be a simple strategy to avoid racemization of the stereocenter during reduction. The developed chemoenzymatic sequential cascade with use of R‐ and S‐selective AMDase variants produced optically pure short‐chain 2‐methylalkanoic acids in moderate to full conversion and gave both enantiomers in excellent enantiopurity (up to 83 % isolated yield and 98 % ee).
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Affiliation(s)
- Junichi Enoki
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitätstraße 150, 44780, Bochum, Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitätstraße 150, 44780, Bochum, Germany
| | - Dirk Tischler
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitätstraße 150, 44780, Bochum, Germany
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 22308522, Yokohama, Japan
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
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6
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Enoki J, Linhorst M, Busch F, Baraibar ÁG, Miyamoto K, Kourist R, Mügge C. Preparation of optically pure flurbiprofen via an integrated chemo-enzymatic synthesis pathway. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Aßmann M, Mügge C, Gaßmeyer SK, Enoki J, Hilterhaus L, Kourist R, Liese A, Kara S. Improvement of the Process Stability of Arylmalonate Decarboxylase by Immobilization for Biocatalytic Profen Synthesis. Front Microbiol 2017; 8:448. [PMID: 28360905 PMCID: PMC5352704 DOI: 10.3389/fmicb.2017.00448] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/03/2017] [Indexed: 02/02/2023] Open
Abstract
The enzyme arylmalonate decarboxylase (AMDase) enables the selective synthesis of enantiopure (S)-arylpropinates in a simple single-step decarboxylation of dicarboxylic acid precursors. However, the poor enzyme stability with a half-life time of about 1.2 h under process conditions is a serious limitation of the productivity, which results in a need for high catalyst loads. By immobilization on an amino C2 acrylate carrier the operational stability of the (S)-selective AMDase variant G74C/M159L/C188G/V43I/A125P/V156L was increased to a half-life of about 8.6 days, which represents a 158-fold improvement. Further optimization was achieved by simple immobilization of the cell lysate to eliminate the cost- and time intensive enzyme purification step.
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Affiliation(s)
- Miriam Aßmann
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | | | - Junichi Enoki
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Lutz Hilterhaus
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
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8
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Liu Q, Zhao C, Huang J, Chen L, Yang K, Gong L, Du Y, Yu C, Wu L, Li X, He Y. Enantioselectivity of d-amino acid oxidase in the presence of ionic liquids. RSC Adv 2017. [DOI: 10.1039/c7ra04687a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper, enantioselectivities of d-amino acid oxidase (DAAO) in ten ionic liquids were investigated in detail.
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9
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
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10
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Ishikawa F, Shirahashi M, Hayakawa H, Yamaguchi A, Hirokawa T, Tsumuraya T, Fujii I. Site-Directed Chemical Mutations on Abzymes: Large Rate Accelerations in the Catalysis by Exchanging the Functionalized Small Nonprotein Components. ACS Chem Biol 2016; 11:2803-2811. [PMID: 27552288 DOI: 10.1021/acschembio.6b00574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Taking advantage of antibody molecules to generate tailor-made binding sites, we propose a new class of protein modifications, termed as "site-directed chemical mutation." In this modification, chemically synthesized catalytic components with a variety of steric and electronic properties can be noncovalently and nongenetically incorporated into specific sites in antibody molecules to induce enzymatic activity. Two catalytic antibodies, 25E2 and 27C1, possess antigen-combining sites which bind catalytic components and act as apoproteins in catalytic reactions. By simply exchanging these components, antibodies 25E2 and 27C1 can catalyze a wide range of chemical transformations including acyl-transfer, β-elimination, aldol, and decarboxylation reactions. Although both antibodies were generated with the same hapten, phosphonate diester 1, they showed different catalytic activity. When phenylacetic acid 4 was used as the catalytic component, 25E2 efficiently catalyzed the elimination reaction of β-haloketone 2, whereas 27C1 showed no catalytic activity. In this work, we focused on the β-elimination reaction and examined the site-directed chemical mutation of 27C1 to induce activity and elucidate the catalytic mechanism. Molecular models showed that the cationic guanidyl group of ArgH52 in 27C1 makes a hydrogen bond with the P═O oxygen in the hapten. This suggested that during β-elimination, ArgH52 of 27C1 would form a salt bridge with the carboxylate of 4, thus destroying reactivity. Therefore, we utilized site-directed chemical mutation to change the charge properties of the catalytic components. When amine components 7-10 were used, 27C1 efficiently catalyzed the β-elimination reaction. It is noteworthy that chemical mutation with secondary amine 8 provided extremely high activity, with a rate acceleration [(kcat/Km 2)/kuncat] of 1 000 000. This catalytic activity likely arises from the proximity effect, plus general-base catalysis associated the electrostatic interactions. In 27C1, the cationic guanidyl group of ArgH52 is spatially close to the nitrogen of the amine components. In this microenvironment, the intrinsic pKa of the amine is perturbed and shifts to a lower pKa, which efficiently abstracts the α-proton during the reaction. This mechanism is consistent with the observed kinetic isotope effect (E2 or E1cB mechanism). Thus, site-directed chemical mutation provides a better understanding of enzyme functions and opens new avenues in biocatalyst research.
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Affiliation(s)
- Fumihiro Ishikawa
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Masato Shirahashi
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Hiroshi Hayakawa
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Asako Yamaguchi
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Takatsugu Hirokawa
- Molecular
Profiling Research Center for Drug Discovery (molprof), Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Takeshi Tsumuraya
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Ikuo Fujii
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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11
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Miyamoto K, Kourist R. Arylmalonate decarboxylase—a highly selective bacterial biocatalyst with unknown function. Appl Microbiol Biotechnol 2016; 100:8621-31. [PMID: 27566691 DOI: 10.1007/s00253-016-7778-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/27/2016] [Accepted: 08/02/2016] [Indexed: 11/24/2022]
Affiliation(s)
- Kenji Miyamoto
- Department for Biosciences and Bioinformatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, 44780, Bochum, Germany.
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12
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Maimanakos J, Chow J, Gaßmeyer SK, Güllert S, Busch F, Kourist R, Streit WR. Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families. Front Microbiol 2016; 7:1332. [PMID: 27610105 PMCID: PMC4996985 DOI: 10.3389/fmicb.2016.01332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/11/2016] [Indexed: 12/11/2022] Open
Abstract
Arylmalonate Decarboxylases (AMDases, EC 4.1.1.76) are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta-, and Gamma-proteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the tripartite tricarboxylate transporters family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99%) of the (R)-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes.
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Affiliation(s)
- Janine Maimanakos
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Sarah K Gaßmeyer
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Simon Güllert
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Florian Busch
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
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13
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Yoshida S, Enoki J, Kourist R, Miyamoto K. Engineered hydrophobic pocket of (S)-selective arylmalonate decarboxylase variant by simultaneous saturation mutagenesis to improve catalytic performance. Biosci Biotechnol Biochem 2015; 79:1965-71. [DOI: 10.1080/09168451.2015.1060844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abstract
A bacterial arylmalonate decarboxylase (AMDase) catalyzes asymmetric decarboxylation of unnatural arylmalonates to produce optically pure (R)-arylcarboxylates without the addition of cofactors. Previously, we designed an AMDase variant G74C/C188S that displays totally inverted enantioselectivity. However, the variant showed a 20,000-fold reduction in activity compared with the wild-type AMDase. Further studies have demonstrated that iterative saturation mutagenesis targeting the active site residues in a hydrophobic pocket of G74C/C188S leads to considerable improvement in activity where all positive variants harbor only hydrophobic substitutions. In this study, simultaneous saturation mutagenesis with a restricted set of amino acids at each position was applied to further heighten the activity of the (S)-selective AMDase variant toward α-methyl-α-phenylmalonate. The best variant (V43I/G74C/A125P/V156L/M159L/C188G) showed 9,500-fold greater catalytic efficiency kcat/Km than that of G74C/C188S. Notably, a high level of decarboxylation of α-(4-isobutylphenyl)-α-methylmalonate by the sextuple variant produced optically pure (S)-ibuprofen, an analgesic compound which showed 2.5-fold greater activity than the (R)-selective wild-type AMDase.
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Affiliation(s)
- Shosuke Yoshida
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Junichi Enoki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Robert Kourist
- Faculty for Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
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14
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Lind MES, Himo F. Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase. ACS Catal 2014. [DOI: 10.1021/cs5009738] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maria E. S. Lind
- Department
of Organic Chemistry
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department
of Organic Chemistry
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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15
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Kourist R, Guterl JK, Miyamoto K, Sieber V. Enzymatic Decarboxylation-An Emerging Reaction for Chemicals Production from Renewable Resources. ChemCatChem 2014. [DOI: 10.1002/cctc.201300881] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Nakamura S. Catalytic enantioselective decarboxylative reactions using organocatalysts. Org Biomol Chem 2013; 12:394-405. [PMID: 24270735 DOI: 10.1039/c3ob42161a] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Catalytic decarboxylative reactions are attractive as biomimetic reactions and environmentally friendly reaction processes. In this review, the origin and recent development of organocatalytic enantioselective decarboxylative reactions of malonic acid half oxy- or thioesters, or β-ketoacids are summarized.
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Affiliation(s)
- Shuichi Nakamura
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan.
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17
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Wada R, Kumon T, Kourist R, Ohta H, Uemura D, Yoshida S, Miyamoto K. Thermally driven asymmetric domino reaction catalyzed by a thermostable esterase and its variants. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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18
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angew Chem Int Ed Engl 2013; 52:5700-25. [PMID: 23526810 DOI: 10.1002/anie.201204077] [Citation(s) in RCA: 357] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 11/07/2022]
Abstract
Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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19
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computerbasiertes Enzymdesign. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Li T, Huo L, Pulley C, Liu A. Decarboxylation mechanisms in biological system. Bioorg Chem 2012; 43:2-14. [PMID: 22534166 DOI: 10.1016/j.bioorg.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/04/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
Abstract
This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.
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Affiliation(s)
- Tingfeng Li
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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21
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Ema T, Nakano Y, Yoshida D, Kamata S, Sakai T. Redesign of enzyme for improving catalytic activity and enantioselectivity toward poor substrates: manipulation of the transition state. Org Biomol Chem 2012; 10:6299-308. [DOI: 10.1039/c2ob25614b] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Abstract
Enantioselective protonation is a common process in biosynthetic sequences. The decarboxylase and esterase enzymes that effect this valuable transformation are able to control both the steric environment around the proton acceptor (typically an enolate) and the proton donor (typically a thiol). Recently, several chemical methods to achieve enantioselective protonation have been developed by exploiting various means of enantiocontrol in different mechanisms. These laboratory transformations have proven useful for the preparation of a number of valuable organic compounds.
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Affiliation(s)
- Justin T Mohr
- Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 164-30, Pasadena, CA 91125, USA
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23
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García-Urdiales E, Alfonso I, Gotor V. Update 1 of: Enantioselective Enzymatic Desymmetrizations in Organic Synthesis. Chem Rev 2011; 111:PR110-80. [DOI: 10.1021/cr100330u] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eduardo García-Urdiales
- Departamento de Química
Orgánica e Inorgánica, Facultad de Química, Universidad
de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain,
and
| | - Ignacio Alfonso
- Departamento de Química Biológica
y Modelización Molecular, Instituto de Química Avanzada
de Cataluña (IQAC, CSIC), Jordi Girona, 18-26, 08034, Barcelona,
Spain
| | - Vicente Gotor
- Departamento de Química
Orgánica e Inorgánica, Facultad de Química, Universidad
de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain,
and
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24
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Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M. Application of Designed Enzymes in Organic Synthesis. Chem Rev 2011; 111:4141-64. [DOI: 10.1021/cr100386u] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gernot A. Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Oliver May
- DSM—Innovative Synthesis BV, Geleen, P.O. Box 18, 6160 MD Geleen, The Netherlands
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25
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Miyauchi Y, Kourist R, Uemura D, Miyamoto K. Dramatically improved catalytic activity of an artificial (S)-selective arylmalonate decarboxylase by structure-guided directed evolution. Chem Commun (Camb) 2011; 47:7503-5. [DOI: 10.1039/c1cc11953b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Obata R, Nakasako M. Structural basis for inverting the enantioselectivity of arylmalonate decarboxylase revealed by the structural analysis of the Gly74Cys/Cys188Ser mutant in the liganded form. Biochemistry 2010; 49:1963-9. [PMID: 20136121 DOI: 10.1021/bi9015605] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arylmalonate decarboxylase catalyzes the enantioselective decarboxylation of alpha-aryl-alpha-methylmalonate to produce optically pure alpha-arylpropionate. The enzyme is comprised of two alpha/beta domains and contains an active site situated between the two domains. The site is formed by Tyr48, Gly74-Thr75-Ser76, Tyr126, and Cys188-Gly189-Gly190 residues. Since it has been observed that the Gly74Cys/Cys188Ser mutation inverts the enantioselectivity of the enzyme, we determined the crystal structure of the Gly74Cys/Cys188Ser mutant in the liganded form at a resolution of 1.45 A to understand the structural basis for this inversion. The overall structure of the enzyme overlapped well with that of the benzylphosphonate-associated wild-type enzyme, and the mutations had little effect on the structure of the active site. A ligand molecule bound to the active site in an unusual semiplanar conformation resembling the planar enediolate reaction intermediate could be assigned as phenyl acetate. The inversion in enantioselectivity by the paired mutation is explained by the mirror symmetry between Cys74 in the mutant and Cys188 of the wild type with respect to the carbon atom in the ligand to be protonated. Comparison of the wild-type and Gly74Cys mutant crystal structures suggested that ligand binding induces a positional shift of the Cys188-Gly189-Gly190 region toward the Gly74-Thr75 pair which provides two oxyanion holes necessary to stabilize the negatively charged enediolate reaction intermediate. The ligand binding also simultaneously induces the formation of a hydrophobic cluster over the active site cleft. Thus, AMDase is proposed to have "open" and "closed" conformations of the active site that are regulated by ligand binding. These results may provide an effective strategy for the rational design to invert the enantioselectivity of enzymes.
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Affiliation(s)
- Rika Obata
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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27
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Harms MJ, Thornton JW. Analyzing protein structure and function using ancestral gene reconstruction. Curr Opin Struct Biol 2010; 20:360-6. [PMID: 20413295 DOI: 10.1016/j.sbi.2010.03.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/22/2010] [Indexed: 01/06/2023]
Abstract
Protein families with functionally diverse members can illuminate the structural determinants of protein function and the process by which protein structure and function evolve. To identify the key amino acid changes that differentiate one family member from another, most studies have taken a horizontal approach, swapping candidate residues between present-day family members. This approach has often been stymied, however, by the fact that shifts in function often require multiple interacting mutations; chimeric proteins are often nonfunctional, either because one lineage has amassed mutations that are incompatible with key residues that conferred a new function on other lineages, or because it lacks mutations required to support those key residues. These difficulties can be overcome by using a vertical strategy, which reconstructs ancestral genes and uses them as the appropriate background in which to study the effects of historical mutations on functional diversification. In this review, we discuss the advantages of the vertical strategy and highlight several exemplary studies that have used ancestral gene reconstruction to reveal the molecular underpinnings of protein structure, function, and evolution.
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Affiliation(s)
- Michael J Harms
- Howard Hughes Medical Institute, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.
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28
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Ema T, Kamata S, Takeda M, Nakano Y, Sakai T. Rational creation of mutant enzyme showing remarkable enhancement of catalytic activity and enantioselectivity toward poor substrates. Chem Commun (Camb) 2010; 46:5440-2. [DOI: 10.1039/c001561j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Okrasa K, Levy C, Wilding M, Goodall M, Baudendistel N, Hauer B, Leys D, Micklefield J. Structure-guided directed evolution of alkenyl and arylmalonate decarboxylases. Angew Chem Int Ed Engl 2009; 48:7691-4. [PMID: 19739187 DOI: 10.1002/anie.200904112] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Krzysztof Okrasa
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, UK
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30
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Antipov E, Cho AE, Klibanov AM. How a single-point mutation in horseradish peroxidase markedly enhances enantioselectivity. J Am Chem Soc 2009; 131:11155-60. [PMID: 19610634 DOI: 10.1021/ja903482u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of all possible mutations at position 178 on the enantioselectivity of yeast surface-bound horseradish peroxidase (HRP) toward chiral phenols has been investigated. In contrast to their wild-type predecessor, most HRP mutants are enantioselective, with the Arg178Glu variant exhibiting the greatest, 25-fold, (S)/(R) preference. Using kinetic analysis of enzymatic oxidation of various substrate analogues and molecular modeling of enzyme-substrate complexes, this enantioselectivity enhancement is attributed to changes in the transition state energy due to electrostatic repulsion between the carboxylates of the enzyme's Glu178 and the substrate's (R)-enantiomer.
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Affiliation(s)
- Eugene Antipov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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31
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Okrasa K, Levy C, Wilding M, Goodall M, Baudendistel N, Hauer B, Leys D, Micklefield J. Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Gerlt JA, Babbitt PC. Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol 2009; 13:10-8. [PMID: 19237310 DOI: 10.1016/j.cbpa.2009.01.014] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 01/14/2009] [Indexed: 11/15/2022]
Abstract
The (re)design of enzymes to catalyze 'new' reactions is a topic of considerable practical and intellectual interest. Directed evolution (random mutagenesis followed by screening/selection) has been used widely to identify novel biocatalysts. However, 'rational' approaches using either natural divergent evolution or computational predictions based on chemical principles have been less successful. This review summarizes recent progress in evolution-based and computation-based (re)design.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, University of Illinois, Urbana, 61801, United States.
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33
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Asymmetric Malonic and Acetoacetic Acid Syntheses – A Century of Enantioselective Decarboxylative Protonations. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800759] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Okrasa K, Levy C, Hauer B, Baudendistel N, Leys D, Micklefield J. Structure and Mechanism of an Unusual Malonate Decarboxylase and Related Racemases. Chemistry 2008; 14:6609-13. [DOI: 10.1002/chem.200800918] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Nakasako M, Obata R, Okubo R, Nakayama S, Miyamoto K, Ohta H. Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:610-3. [PMID: 18607088 DOI: 10.1107/s1744309108014723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 05/15/2008] [Indexed: 11/11/2022]
Abstract
Arylmalonate decarboxylase catalyses the enantioselective decarboxylation of alpha-aryl-alpha-methylmalonates to produce optically pure alpha-arylpropionates. The enzyme was crystallized with ammonium sulfate under alkaline pH conditions with the aim of understanding the mechanism of the enantioselective reaction. X-ray diffraction data collected to a resolution of 3.0 A at cryogenic temperature showed that the crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 83.13, b = 99.62, c = 139.64 A. This suggested that the asymmetric unit would contain between four and six molecules. Small-angle X-ray scattering revealed that the enzyme exists as a monomer in solution. Thus, the assembly of molecules in the asymmetric unit was likely to have been induced during the crystallization process.
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Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522, Japan.
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36
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Active-Site Mobility Revealed by the Crystal Structure of Arylmalonate Decarboxylase from Bordetella bronchiseptica. J Mol Biol 2008; 377:386-94. [DOI: 10.1016/j.jmb.2007.12.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/18/2007] [Accepted: 12/26/2007] [Indexed: 11/19/2022]
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37
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Hall M, Stueckler C, Ehammer H, Pointner E, Oberdorfer G, Gruber K, Hauer B, Stuermer R, Kroutil W, Macheroux P, Faber K. Asymmetric Bioreduction of CC Bonds using Enoate Reductases OPR1, OPR3 and YqjM: Enzyme-Based Stereocontrol. Adv Synth Catal 2008. [DOI: 10.1002/adsc.200700458] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Toscano MD, Woycechowsky KJ, Hilvert D. Minimalist active-site redesign: teaching old enzymes new tricks. Angew Chem Int Ed Engl 2007; 46:3212-36. [PMID: 17450624 DOI: 10.1002/anie.200604205] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although nature evolves its catalysts over millions of years, enzyme engineers try to do it a bit faster. Enzyme active sites provide highly optimized microenvironments for the catalysis of biologically useful chemical transformations. Consequently, changes at these centers can have large effects on enzyme activity. The prediction and control of these effects provides a promising way to access new functions. The development of methods and strategies to explore the untapped catalytic potential of natural enzyme scaffolds has been pushed by the increasing demand for industrial biocatalysts. This Review describes the use of minimal modifications at enzyme active sites to expand their catalytic repertoires, including targeted mutagenesis and the addition of new reactive functionalities. Often, a novel activity can be obtained with only a single point mutation. The many successful examples of active-site engineering through minimal mutations give useful insights into enzyme evolution and open new avenues in biocatalyst research.
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Affiliation(s)
- Miguel D Toscano
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, Switzerland
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39
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Hall M, Stueckler C, Kroutil W, Macheroux P, Faber K. Asymmetric Bioreduction of Activated Alkenes Using Cloned 12-Oxophytodienoate Reductase Isoenzymes OPR-1 and OPR-3 fromLycopersicon esculentum (Tomato): A Striking Change of Stereoselectivity. Angew Chem Int Ed Engl 2007; 46:3934-7. [PMID: 17431865 DOI: 10.1002/anie.200605168] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mélanie Hall
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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40
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Hall M, Stueckler C, Kroutil W, Macheroux P, Faber K. Asymmetric Bioreduction of Activated Alkenes Using Cloned 12-Oxophytodienoate Reductase Isoenzymes OPR-1 and OPR-3 fromLycopersicon esculentum (Tomato): A Striking Change of Stereoselectivity. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605168] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Miyamoto K, Tsutsumi T, Terao Y, Ohta H. Stereochemistry of Decarboxylation of Arylmalonate Catalyzed by Mutant Enzymes. CHEM LETT 2007. [DOI: 10.1246/cl.2007.656] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Toscano M, Woycechowsky K, Hilvert D. Minimale Umgestaltung aktiver Enzymtaschen – wie man alten Enzymen neue Kunststücke beibringt. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604205] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Terao Y, Ijima Y, Miyamoto K, Ohta H. Inversion of enantioselectivity of arylmalonate decarboxylase via site-directed mutation based on the proposed reaction mechanism. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.molcatb.2006.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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Terao Y, Miyamoto K, Ohta H. Improvement of the activity of arylmalonate decarboxylase by random mutagenesis. Appl Microbiol Biotechnol 2006; 73:647-53. [PMID: 16865343 DOI: 10.1007/s00253-006-0518-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/20/2006] [Accepted: 05/23/2006] [Indexed: 11/26/2022]
Abstract
Arylmalonate decarboxylase (EC 4.1.1.76) catalyzes enantioselective decarboxylation of alpha-aryl-alpha-methylmalonates to give optically pure alpha-arylpropionates. Recently, we have succeeded in creating a double mutant enzyme that gave opposite enantionmer as the product. Unfortunately, however, the activity of the mutant decreased far lower than that of the native enzyme. Thus, we performed the directed evolution of the mutant via the random mutagenesis method employing the mutator strain Escherichia coli XL1-Red. About 50,000 mutants were screened on color assay plate, and one mutant with higher activity was obtained. Gene analysis of this mutant indicated that the obtained enzyme had an S36N mutation in addition to its original G74C/C188S mutations. The activity of the triple mutant enzyme was tenfold higher than that of the starting doubly mutated enzyme.
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Affiliation(s)
- Y Terao
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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Broering JM, Hill EM, Hallett JP, Liotta CL, Eckert CA, Bommarius AS. Biocatalytic Reaction And Recycling by Using CO2-Induced Organic–Aqueous Tunable Solvents. Angew Chem Int Ed Engl 2006; 45:4670-3. [PMID: 16789050 DOI: 10.1002/anie.200600862] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James M Broering
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332-0363, USA
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Biocatalytic Reaction And Recycling by Using CO2-Induced Organic–Aqueous Tunable Solvents. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Seitz T, Baudoux J, Bekolo H, Cahard D, Plaquevent JC, Lasne MC, Rouden J. Organocatalyzed route to enantioenriched pipecolic esters: decarboxylation of an aminomalonate hemiester. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.04.062] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Terao Y, Miyamoto K, Ohta H. Introduction of single mutation changes arylmalonate decarboxylase to racemase. Chem Commun (Camb) 2006:3600-2. [PMID: 17047777 DOI: 10.1039/b607211a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The introduction of only one mutation based on the estimated reaction mechanism endowed arylmalonate decarboxylase with a racemase activity, which catalyses racemisation of alpha-arylpropionates.
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Affiliation(s)
- Yosuke Terao
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
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Ema T, Fujii T, Ozaki M, Korenaga T, Sakai T. Rational control of enantioselectivity of lipase by site-directed mutagenesis based on the mechanism. Chem Commun (Camb) 2005:4650-1. [PMID: 16175280 DOI: 10.1039/b508244g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enantioselectivity of a Burkholderia cepacia lipase toward secondary alcohols could be both increased and decreased rationally by introducing only a single mutation on the basis of the mechanism proposed previously.
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Affiliation(s)
- Tadashi Ema
- Department of Applied Chemistry, Faculty of Engineering, Okayama University, Tsushima, Okayama 700-8530, Japan.
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