1
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Reetz MT. Breakthrough in the chemoenzymatic transformation of CO 2 for the sustainable artificial synthesis of hexoses with complete control of stereochemistry. Sci Bull (Beijing) 2023; 68:2291-2292. [PMID: 37657972 DOI: 10.1016/j.scib.2023.08.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Affiliation(s)
- Manfred T Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Biocatalysis Section, Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany.
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2
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Yu H, Zhang X, Acevedo-Rocha CG, Li A, Reetz MT. Protein engineering using mutability landscapes: Controlling site-selectivity of P450-catalyzed steroid hydroxylation. Methods Enzymol 2023; 693:191-229. [PMID: 37977731 DOI: 10.1016/bs.mie.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Directed evolution and rational design have been used widely in engineering enzymes for their application in synthetic organic chemistry and biotechnology. With stereoselectivity playing a crucial role in catalysis for the synthesis of valuable chemical and pharmaceutical compounds, rational design has not achieved such wide success in this specific area compared to directed evolution. Nevertheless, one bottleneck of directed evolution is the laborious screening efforts and the observed trade-offs in catalytic profiles. This has motivated researchers to develop more efficient protein engineering methods. As a prime approach, mutability landscaping avoids such trade-offs by providing more information of sequence-function relationships. Here, we describe an application of this efficient protein engineering method to improve the regio-/stereoselectivity and activity of P450BM3 for steroid hydroxylation, while keeping the mutagenesis libraries small so that they will require only minimal screening.
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Affiliation(s)
- Huili Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China
| | - Xiaodong Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China
| | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of life science, Hubei University, Wuhan, P.R. China.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, Muelheim, Germany; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, P. R. China.
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3
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Reetz MT. Dyotropic Rearrangements in Organic Solvents, in the Gas Phase, and in Enzyme Catalysis. Isr J Chem 2023. [DOI: 10.1002/ijch.202200122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
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4
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Li JK, Qu G, Li X, Tian Y, Cui C, Zhang FG, Zhang W, Ma JA, Reetz MT, Sun Z. Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles. Nat Commun 2022; 13:7813. [PMID: 36535947 PMCID: PMC9763437 DOI: 10.1038/s41467-022-35468-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Chiral heterocyclic compounds are needed for important medicinal applications. We report an in silico strategy for the biocatalytic synthesis of chiral N- and O-heterocycles via Baldwin cyclization modes of hydroxy- and amino-substituted epoxides and oxetanes using the limonene epoxide hydrolase from Rhodococcus erythropolis. This enzyme normally catalyzes hydrolysis with formation of vicinal diols. Firstly, the required shutdown of the undesired natural water-mediated ring-opening is achieved by rational mutagenesis of the active site. In silico enzyme design is then continued with generation of the improved mutants. These variants prove to be versatile catalysts for preparing chiral N- and O-heterocycles with up to 99% conversion, and enantiomeric ratios up to 99:1. Crystal structural data and computational modeling reveal that Baldwin-type cyclizations, catalyzed by the reprogrammed enzyme, are enabled by reshaping the active-site environment that directs the distal RHN and HO-substituents to be intramolecular nucleophiles.
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Affiliation(s)
- Jun-Kuan Li
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China ,grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Ge Qu
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Xu Li
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Yuchen Tian
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China
| | - Chengsen Cui
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Fa-Guang Zhang
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China
| | - Wuyuan Zhang
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Jun-An Ma
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China
| | - Manfred T. Reetz
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,grid.419607.d0000 0001 2096 9941Biocatalysis Section, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Zhoutong Sun
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
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Abstract
This review outlines recent developments in protein engineering of stereo‐ and regioselective enzymes, which are of prime interest in organic and pharmaceutical chemistry as well as biotechnology. The widespread application of enzymes was hampered for decades due to limited enantio‐, diastereo‐ and regioselectivity, which was the reason why most organic chemists were not interested in biocatalysis. This attitude began to change with the advent of semi‐rational directed evolution methods based on focused saturation mutagenesis at sites lining the binding pocket. Screening constitutes the labor‐intensive step (bottleneck), which is the reason why various research groups are continuing to develop techniques for the generation of small and smart mutant libraries. Rational enzyme design, traditionally an alternative to directed evolution, provides small collections of mutants which require minimal screening. This approach first focused on thermostabilization, and did not enter the field of stereoselectivity until later. Computational guides such as the Rosetta algorithms, HotSpot Wizard metric, and machine learning (ML) contribute significantly to decision making. The newest advancements show that semi‐rational directed evolution such as CAST/ISM and rational enzyme design no longer develop on separate tracks, instead, they have started to merge. Indeed, researchers utilizing the two approaches have learned from each other. Today, the toolbox of organic chemists includes enzymes, primarily because the possibility of controlling stereoselectivity by protein engineering has ensured reliability when facing synthetic challenges. This review was also written with the hope that undergraduate and graduate education will include enzymes more so than in the past.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut fur Kohlenforschung, Biocatalysis, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, GERMANY
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Dong Y, Li T, Zhang S, Sanchis J, Yin H, Ren J, Sheng X, Li G, Reetz MT. Biocatalytic Baeyer–Villiger Reactions: Uncovering the Source of Regioselectivity at Each Evolutionary Stage of a Mutant with Scrutiny of Fleeting Chiral Intermediates. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yijie Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
- Key Laboratory of Agricultural Microbiomics and Precision Application − Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Tang Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, PR China
| | - Shiqing Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P.R. China
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, PR China
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P.R. China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim 45470, Germany
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Reetz MT, König G. n
‐Butanol: An Ecologically and Economically Viable Extraction Solvent for Isolating Polar Products from Aqueous Solutions. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin China
| | - Gerhard König
- Centre for Enzyme Innovation University of Portsmouth St Michael's Building Portsmouth PO1 2DT United Kingdom
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Reetz MT. Effective Mentoring and the Problem of Assessing Quality in Science. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 DE-45470 Mülheim an der Ruhr Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue Tianjin 300308 P. R. China
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Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
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10
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Cadet F, Fontaine N, Li G, Sanchis J, Chong MNF, Pandjaitan R, Vetrivel I, Offmann B, Reetz MT. Publisher Correction: A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes. Sci Rep 2021; 11:8357. [PMID: 33846404 PMCID: PMC8041870 DOI: 10.1038/s41598-021-86884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Frédéric Cadet
- PEACCEL, Protein Engineering Accelerator, Paris, France.
| | | | - Guangyue Li
- Department of Chemistry, Philipps-University, 35032, Marburg, Germany
| | - Joaquin Sanchis
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Australia
| | | | | | | | - Bernard Offmann
- UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, Université de Nantes, Nantes, France
| | - Manfred T Reetz
- Department of Chemistry, Philipps-University, 35032, Marburg, Germany.,Max-Planck-Institut Fuer Kohlenforschung, 45470, Mülheim, Germany
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11
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Li G, Qin Y, Fontaine NT, Ng Fuk Chong M, Maria‐Solano MA, Feixas F, Cadet XF, Pandjaitan R, Garcia‐Borràs M, Cadet F, Reetz MT. Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation. Chembiochem 2021; 22:904-914. [PMID: 33094545 PMCID: PMC7984044 DOI: 10.1002/cbic.202000612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/22/2020] [Indexed: 12/15/2022]
Abstract
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved high protein robustness that can resist unfolding with concomitant detrimental aggregation. Fourier transform (FT) allows us to take into account the order of the protein sequence and the nonlinear interactions between positions, and thus to grasp epistatic phenomena. The innov'SAR approach is interpolative, extrapolative and makes outside-the-box, predictions not found in other state-of-the-art ML or deep learning approaches. Equally significant is the finding that our approach to ML in the present context, flanked by advanced molecular dynamics simulations, uncovers the connection between epistatic mutational interactions and protein robustness.
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Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Youcai Qin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Nicolas T. Fontaine
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Matthieu Ng Fuk Chong
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Miguel A. Maria‐Solano
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Xavier F. Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Rudy Pandjaitan
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Frederic Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Manfred T. Reetz
- Department of ChemistryPhilipps-Universität35032MarburgGermany) .
- Max-Planck-Institut fuer Kohlenforschung45470MülheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Avenue, Tianjin Airport Economic Area300308TianjinP. R. China
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Lehmann U, Goddard R, Tonner R, Reetz MT. Towards self-doping multimetal porphyrin systems. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An approach for the possible production of novel bimetallic self-doped porphyrin-based compounds of potential interest in material science is reported. Heating Cu(II)tetraphenylporphyrin (TPPCu) with chromocene at 120°C in benzonitrile affords the crystalline multimetal porphyrin system TPPCu/TPPCr in good yield. The X-ray single crystal structural analysis reveals a random distribution of TPPCu and TPPCr, with a Cu:Cr ratio of 71(2):29(2)%. Exploratory DFT calculations of TPPCu/TPPCr indicate little if any electron transfer. In contrast, calculations of a hypothetical cationic TPPCu/TPPRu system indicates the possibility of self-doping.
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Affiliation(s)
- Udo Lehmann
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| | - Richard Goddard
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| | - Ralf Tonner
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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Li A, Acevedo‐Rocha CG, D'Amore L, Chen J, Peng Y, Garcia‐Borràs M, Gao C, Zhu J, Rickerby H, Osuna S, Zhou J, Reetz MT. Regio- and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Angew Chem Int Ed Engl 2020; 59:12499-12505. [PMID: 32243054 PMCID: PMC7384163 DOI: 10.1002/anie.202003139] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/31/2020] [Indexed: 01/08/2023]
Abstract
Steroidal C7β alcohols and their respective esters have shown significant promise as neuroprotective and anti-inflammatory agents to treat chronic neuronal damage like stroke, brain trauma, and cerebral ischemia. Since C7 is spatially far away from any functional groups that could direct C-H activation, these transformations are not readily accessible using modern synthetic organic techniques. Reported here are P450-BM3 mutants that catalyze the oxidative hydroxylation of six different steroids with pronounced C7 regioselectivities and β stereoselectivities, as well as high activities. These challenging transformations were achieved by a focused mutagenesis strategy and application of a novel technology for protein library construction based on DNA assembly and USER (Uracil-Specific Excision Reagent) cloning. Upscaling reactions enabled the purification of the respective steroidal alcohols in moderate to excellent yields. The high-resolution X-ray structure and molecular dynamics simulations of the best mutant unveil the origin of regio- and stereoselectivity.
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Affiliation(s)
- Aitao Li
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | | | - Lorenzo D'Amore
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesShanghai200032P. R. China
| | - Yaqin Peng
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Chenghua Gao
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Jinmei Zhu
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Harry Rickerby
- LabGeniusG.01-06 Cocoa Studios100 Drummond RdLondonSE16 4DGUK
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesShanghai200032P. R. China
| | - Manfred T. Reetz
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470MuelheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th AvenueTianjin300308P. R. China
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15
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Li A, Acevedo‐Rocha CG, D'Amore L, Chen J, Peng Y, Garcia‐Borràs M, Gao C, Zhu J, Rickerby H, Osuna S, Zhou J, Reetz MT. Regio‐ and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003139] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Aitao Li
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | | | - Lorenzo D'Amore
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Yaqin Peng
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Chenghua Gao
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Jinmei Zhu
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Harry Rickerby
- LabGenius G.01-06 Cocoa Studios 100 Drummond Rd London SE16 4DG UK
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue Tianjin 300308 P. R. China
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201901491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Deutschland
- Department of Chemistry, Hans-Meerwein-Straße 4 Philipps-Universität 35032 Marburg Deutschland
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17
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. Angew Chem Int Ed Engl 2020; 59:13204-13231. [PMID: 31267627 DOI: 10.1002/anie.201901491] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Department of Chemistry, Hans-Meerwein-Strasse 4 Philipps-University 35032 Marburg Germany
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18
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Wang JB, Huang Q, Peng W, Wu P, Yu D, Chen B, Wang B, Reetz MT. P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species? J Am Chem Soc 2020; 142:2068-2073. [PMID: 31927987 PMCID: PMC7307895 DOI: 10.1021/jacs.9b13061] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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While the mechanism of the P450-catalyzed
oxidative hydroxylation of organic compounds has been studied in detail
for many years, less is known about sulfoxidation. Depending upon
the structure of the respective substrate, heme-Fe=O (Cpd I),
heme–Fe(III)–OOH (Cpd 0), and heme–Fe(III)–H2O2 (protonated Cpd 0) have been proposed as reactive
intermediates. In the present study, we consider the transformation
of isosteric substrates via sulfoxidation and oxidative hydroxylation,
respectively, catalyzed by regio- and enantioselective mutants of
P450-BM3 which were constructed by directed evolution. 1-Thiochromanone
and 1-tetralone were used as the isosteric substrates because, unlike
previous studies involving fully flexible compounds such as thia-fatty
acids and fatty acids, respectively, these compounds are rigid and
cannot occur in a multitude of different conformations and binding
modes in the large P450-BM3 binding pocket. The experimental results
comprising activity and regio- and enantioselectivity, flanked by
molecular dynamics computations within a time scale of 300 ns and
QM/MM calculations of transition-state energies, unequivocally show
that heme-Fe=O (Cpd I) is the common catalytically active intermediate
in both sulfoxidation and oxidative hydroxylation.
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Affiliation(s)
| | | | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | | | | | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | - Manfred T Reetz
- Chemistry Department , Philipps-University , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany.,Max-Planck Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim , Germany
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19
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Li A, Qu G, Sun Z, Reetz MT. Statistical Analysis of the Benefits of Focused Saturation Mutagenesis in Directed Evolution Based on Reduced Amino Acid Alphabets. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02548] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, 368 Youyi Road, Wuchang Wuhan 430062, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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20
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Xu J, Cen Y, Singh W, Fan J, Wu L, Lin X, Zhou J, Huang M, Reetz MT, Wu Q. Stereodivergent Protein Engineering of a Lipase To Access All Possible Stereoisomers of Chiral Esters with Two Stereocenters. J Am Chem Soc 2019; 141:7934-7945. [DOI: 10.1021/jacs.9b02709] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jian Xu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
| | - Yixin Cen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Warispreet Singh
- School of Chemistry and Chemical Engineering, Queen’s University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, U.K
| | - Jiajie Fan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
| | - Lian Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Xianfu Lin
- Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen’s University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, U.K
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
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21
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Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural Sciences Beijing 100081 People's Republic of China
| | - Yijie Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural Sciences Beijing 100081 People's Republic of China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie der Philipps-Universität Hans-Meerwein-Strasse 35032 Marburg Germany
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22
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Abstract
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A unique P450 monooxygenase–peroxygenase
mutual benefit
system was designed as the core element in the construction of a biocatalytic
cascade reaction sequence leading from 3-phenyl propionic acid to
(R)-phenyl glycol. In this system, P450 monooxygenase
(P450-BM3) and P450 peroxygenase (OleTJE) not only function
as catalysts for the crucial initial reactions, they also ensure an
internal in situ H2O2 recycle mechanism that
avoids its accumulation and thus prevents possible toxic effects.
By directed evolution of P450-BM3 as the catalyst in the enantioselective
epoxidation of the styrene-intermediate, formed from 3-phenyl propionic
acid, and the epoxide hydrolase ANEH for final hydrolytic ring opening,
(R)-phenyl glycol and 9 derivatives thereof were
synthesized from the respective carboxylic acids in one-pot processes
with high enantioselectivity.
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Affiliation(s)
- Da Yu
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering , Hunan Normal University , 410081 Changsha , People's Republic of China.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering , Hunan Normal University , 410081 Changsha , People's Republic of China
| | - Jian-Bo Wang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering , Hunan Normal University , 410081 Changsha , People's Republic of China.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering , Hunan Normal University , 410081 Changsha , People's Republic of China
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Muelheim an der Ruhr , Germany.,Fachbereich Chemie, Philipps-Universität Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
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23
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Abstract
Transition metal catalysts mediate a wide variety of chemo-, stereo-, and regioselective transformations, and therefore play a pivotal role in modern synthetic organic chemistry. Steric and electronic effects of ligands provide organic chemists with an exceedingly useful tool. More than four decades ago, chemists began to think about a different approach, namely, embedding achiral ligand/metal moieties covalently or noncovalently in protein hosts with formation of artificial metalloenzymes. While structurally fascinating, this approach led in each case only to a single (bio)catalyst, with its selectivity and activity being a matter of chance. In order to solve this fundamental problem, my group proposed in 2000-2002 the idea of directed evolution of artificial metalloenzymes. In earlier studies, we had already demonstrated that directed evolution of enzymes constitutes a viable method for enhancing and inverting the stereoselectivity of enzymes as catalysts in organic chemistry. We speculated that it should also be possible to manipulate selectivity and activity of artificial metalloenzymes, which would provide organic chemists with a tool for optimizing essentially any transition metal catalyzed reaction type. In order to put this vision into practice, we first turned to the Whitesides system for artificial metalloenzyme formation, comprising a biotinylated diphosphine/Rh moiety, which is anchored noncovalently to avidin or streptavidin. Following intensive optimization, proof of principle was finally demonstrated in 2006, which opened the door to a new research area. This personal Account critically assesses these early studies as well as subsequent efforts from my group focusing on different protein scaffolds, and includes briefly some of the most important current contributions of other groups. Two primary messages emerge: First, since organic chemists continue to be extremely good at designing and implementing man-made transition metal catalysts, often on a large scale, those scientists that are active in the equally intriguing field of directed evolution of artificial metalloenzymes should be moderate when generalizing claims. All factors required for a truly viable catalytic system need to be considered, especially activity and ease of upscaling. Second, the most exciting and thus far very rare cases of directed evolution of artificial metalloenzymes are those that focus on selective transformations that are not readily possible using state of the art transition metal catalysts.
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Affiliation(s)
- Manfred T. Reetz
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim Germany
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24
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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25
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Zhou H, Wang B, Wang F, Yu X, Ma L, Li A, Reetz MT. Back Cover: Chemo‐ and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase (Angew. Chem. Int. Ed. 3/2019). Angew Chem Int Ed Engl 2019. [DOI: 10.1002/anie.201813834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hangyu Zhou
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational ChemistryCollege of Chemistry and Chemical EngineeringXiamen University Xiamen 360015 P. R. China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Xiaojuan Yu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of ChemistryPhilipps-University Hans-Meerwein-Strasse 4 35032 Marburg Germany
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26
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Zhou H, Wang B, Wang F, Yu X, Ma L, Li A, Reetz MT. Chemo‐ and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201813834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hangyu Zhou
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational ChemistryCollege of Chemistry and Chemical EngineeringXiamen University Xiamen 360015 P. R. China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Xiaojuan Yu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-ResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei University Wuhan 430062 P. R. China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of ChemistryPhilipps-University Hans-Meerwein-Strasse 4 35032 Marburg Germany
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27
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Zhou H, Wang B, Wang F, Yu X, Ma L, Li A, Reetz MT. Chemo- and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase. Angew Chem Int Ed Engl 2018; 58:764-768. [PMID: 30511432 DOI: 10.1002/anie.201812093] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/06/2018] [Indexed: 11/10/2022]
Abstract
Hydroquinone (HQ) is produced commercially from benzene by multi-step Hock-type processes with equivalent amounts of acetone as side-product. We describe an efficient biocatalytic alternative using the cytochrome P450-BM3 monooxygenase. Since the wildtype enzyme does not accept benzene, a semi-rational protein engineering strategy was developed. Highly active mutants were obtained which transform benzene in a one-pot sequence first into phenol and then regioselectively into HQ without any overoxidation. A computational study shows that the chemoselective oxidation of phenol by the P450-BM3 variant A82F/A328F leads to the regioselective formation of an epoxide intermediate at the C3=C4 double bond, which departs from the binding pocket and then undergoes fragmentation in aqueous medium with exclusive formation of HQ. As a practical application, an E. coli designer cell system was constructed, which enables the cascade transformation of benzene into the natural product arbutin, which has anti-inflammatory and anti-bacterial activities.
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Affiliation(s)
- Hangyu Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, P. R. China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P. R. China
| | - Xiaojuan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P. R. China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P. R. China
| | - Manfred T Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany.,Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
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28
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Zhou H, Wang B, Wang F, Yu X, Ma L, Li A, Reetz MT. Chemo- and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812093] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hangyu Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; School of Life Sciences; Hubei University; Wuhan 430062 P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen 360015 P. R. China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; School of Life Sciences; Hubei University; Wuhan 430062 P. R. China
| | - Xiaojuan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; School of Life Sciences; Hubei University; Wuhan 430062 P. R. China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; School of Life Sciences; Hubei University; Wuhan 430062 P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; School of Life Sciences; Hubei University; Wuhan 430062 P. R. China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-University; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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29
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Cadet F, Fontaine N, Li G, Sanchis J, Ng Fuk Chong M, Pandjaitan R, Vetrivel I, Offmann B, Reetz MT. A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes. Sci Rep 2018; 8:16757. [PMID: 30425279 PMCID: PMC6233173 DOI: 10.1038/s41598-018-35033-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/26/2018] [Indexed: 11/09/2022] Open
Abstract
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have facilitated the prediction of protein properties and the identification of improved mutants. However, epistatic phenomena constitute an obstacle which can impair the predictions in protein engineering. We present an innovative sequence-activity relationship (innov'SAR) methodology based on digital signal processing combining wet-lab experimentation and computational protein design. In our machine learning approach, a predictive model is developed to find the resulting property of the protein when the n single point mutations are permuted (2n combinations). The originality of our approach is that only sequence information and the fitness of mutants measured in the wet-lab are needed to build models. We illustrate the application of the approach in the case of improving the enantioselectivity of an epoxide hydrolase from Aspergillus niger. n = 9 single point mutants of the enzyme were experimentally assessed for their enantioselectivity and used as a learning dataset to build a model. Based on combinations of the 9 single point mutations (29), the enantioselectivity of these 512 variants were predicted, and candidates were experimentally checked: better mutants with higher enantioselectivity were indeed found.
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Affiliation(s)
- Frédéric Cadet
- PEACCEL, Protein Engineering Accelerator, Paris, France.
| | | | - Guangyue Li
- Department of Chemistry, Philipps-University, 35032, Marburg, Germany
| | - Joaquin Sanchis
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Australia
| | | | | | | | - Bernard Offmann
- UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, Université de Nantes, Nantes, France
| | - Manfred T Reetz
- Department of Chemistry, Philipps-University, 35032, Marburg, Germany
- Max-Planck-Institut fuer Kohlenforschung, 45470, Mülheim, Germany
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Acevedo‐Rocha CG, Sun Z, Reetz MT. Clarifying the Difference between Iterative Saturation Mutagenesis as a Rational Guide in Directed Evolution and OmniChange as a Gene Mutagenesis Technique. Chembiochem 2018; 19:2542-2544. [PMID: 30408315 DOI: 10.1002/cbic.201800372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - Zhoutong Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Department of ChemistryPhilipps University 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
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Dong Y, Yao P, Cui Y, Wu Q, Zhu D, Li G, Reetz MT. Manipulating the stereoselectivity of a thermostable alcohol dehydrogenase by directed evolution for efficient asymmetric synthesis of arylpropanols. Biol Chem 2018; 400:313-321. [DOI: 10.1515/hsz-2018-0299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/30/2018] [Indexed: 01/24/2023]
Abstract
Abstract
Chiral arylpropanols are valuable components in important pharmaceuticals and fragrances, which is the motivation for previous attempts to prepare these building blocks enantioselectively in asymmetric processes using either enzymes or transition metal catalysts. Thus far, enzymes used in kinetic resolution proved to be best, but several problems prevented ecologically and economically viable processes from being developed. In the present study, directed evolution was applied to the thermostable alcohol dehydrogenase TbSADH in the successful quest to obtain mutants that are effective in the dynamic reductive kinetic resolution (DYRKR) of racemic arylpropanals. Using rac-2-phenyl-1-propanal in a model reaction, (S)- and (R)-selective mutants were evolved which catalyzed DYRKR of this racemic substrate with formation of the respective (S)- and (R)-alcohols in essentially enantiomerically pure form. This was achieved on the basis of an unconventional form of iterative saturation mutagenesis (ISM) at randomization sites lining the binding pocket using a reduced amino acid alphabet. The best mutants were also effective in the DYRKR of several other structurally related racemic aldehydes.
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Affiliation(s)
- Yijie Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture , Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , China
| | - Yunfeng Cui
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture , Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100081 , China
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim , Germany
- Department of Chemistry , Philipps University , Hans-Meerwein-Strasse 4 , D-35032 Marburg , Germany
| | - Manfred T. Reetz
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , China
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim , Germany
- Department of Chemistry , Philipps University , Hans-Meerwein-Strasse 4 , D-35032 Marburg , Germany
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She W, Ni J, Shui K, Wang F, He R, Xue J, Reetz MT, Li A, Ma L. Rapid and Error-Free Site-Directed Mutagenesis by a PCR-Free In Vitro CRISPR/Cas9-Mediated Mutagenic System. ACS Synth Biol 2018; 7:2236-2244. [PMID: 30075075 DOI: 10.1021/acssynbio.8b00245] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The quality and efficiency of any PCR-based mutagenesis technique may not be optimal due to, among other things, amino acid bias, which means that the development of efficient PCR-free methods is desirable. Here, we present a highly efficient in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants in a PCR-free manner. First, it involves plasmid digestion by utilizing a complex of Cas9 with specific single guide RNA (sgRNA) followed by degradation with T5 exonuclease to generate a 15 nt homologous region. Second, primers containing the desired mutations are annealed to form the double-stranded DNA fragments, which are then ligated into the linearized plasmid. In theory, neither the size of the target plasmid nor the unavailable restriction enzyme site poses any problems that may arise in traditional techniques. In this study, single and multiple site-directed mutagenesis were successfully performed even for a large size plasmid (up to 9.0 kb). Moreover, a PCR-free site-saturation mutagenesis library on single site and two adjacent sites of a green fluorescent protein was also generated with promising results. This demonstrates the great potential of the ICM system for creating high-quality mutant libraries in directed evolution as an alternative to PCR-based saturation mutagenesis, thus facilitating research on synthetic biology.
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Affiliation(s)
- Wenwen She
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jing Ni
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fei Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ruyi He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jinhui Xue
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
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Li A, Sun Z, Reetz MT. Solid-Phase Gene Synthesis for Mutant Library Construction: The Future of Directed Evolution? Chembiochem 2018; 19:2023-2032. [PMID: 30044530 DOI: 10.1002/cbic.201800339] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of, Bio-resources; Hubei Key Laboratory of Industrial Biotechnology; College of Life Sciences; Hubei University; 368 Youyi Road Wuchang Wuhan 430062 China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
- Department of Chemistry; Philipps University; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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Li G, Garcia-Borràs M, Furst MJLJ, Ilie A, Fraaije MW, Houk KN, Reetz MT. Overriding Traditional Electronic Effects in Biocatalytic Baeyer-Villiger Reactions by Directed Evolution. J Am Chem Soc 2018; 140:10464-10472. [PMID: 30044629 PMCID: PMC6314816 DOI: 10.1021/jacs.8b04742] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Controlling the regioselectivity of Baeyer-Villiger (BV) reactions remains an ongoing issue in organic chemistry, be it by synthetic catalysts or enzymes of the type Baeyer-Villiger monooxygenases (BVMOs). Herein, we address the challenging problem of switching normal to abnormal BVMO regioselectivity by directed evolution using three linear ketones as substrates, which are not structurally biased toward abnormal reactivity. Upon applying iterative saturation mutagenesis at sites lining the binding pocket of the thermostable BVMO from Thermocrispum municipale DSM 44069 (TmCHMO) and using 4-phenyl-2-butanone as substrate, the regioselectivity was reversed from 99:1 (wild-type enzyme in favor of the normal product undergoing 2-phenylethyl migration) to 2:98 in favor of methyl migration when applying the best mutant. This also stands in stark contrast to the respective reaction using the synthetic reagent m-CPBA, which provides solely the normal product. Reversal of regioselectivity was also achieved in the BV reaction of two other linear ketones. Kinetic parameters and melting temperatures revealed that most of the evolved mutants retained catalytic activity, as well as thermostability. In order to shed light on the origin of switched regioselectivity in reactions of 4-phenyl-2-butanone and phenylacetone, extensive QM/MM and MD simulations were performed. It was found that the mutations introduced by directed evolution induce crucial changes in the conformation of the respective Criegee intermediates and transition states in the binding pocket of the enzyme. In mutants that destabilize the normally preferred migration transition state, a reversal of regioselectivity is observed. This conformational control of regioselectivity overrides electronic control, which normally causes preferential migration of the group that is best able to stabilize positive charge. The results can be expected to aid future protein engineering of BVMOs.
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Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agriproduct Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Max-Planck-Institut fürKohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Maximilian J. L. J. Furst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Adriana Ilie
- Max-Planck-Institut fürKohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Manfred T. Reetz
- Max-Planck-Institut fürKohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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35
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König G, Reetz MT, Thiel W. 1-Butanol as a Solvent for Efficient Extraction of Polar Compounds from Aqueous Medium: Theoretical and Practical Aspects. J Phys Chem B 2018; 122:6975-6988. [PMID: 29897756 DOI: 10.1021/acs.jpcb.8b02877] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The extraction of polar molecules from aqueous solution is a challenging task in organic synthesis. 1-Butanol has been used sporadically as an eluent for polar molecules, but it is unclear which molecular features drive its efficiency. Here, we employ free energy simulations to study the partitioning of 15 solutes between water and 1-butanol. The simulations demonstrate that the high affinity of polar molecules to the wet 1-butanol phase is associated with its nanostructure. Small inverse micelles of water are able to accommodate polar solutes and locally mimic an aqueous environment. We verify the simulations based on partition coefficients between water and 1-octanol, and include a blind prediction of the water/1-butanol partition coefficient of cyclohexane-1,2-diol. The calculations are in excellent agreement with experiment, reaching root-mean-square deviations below 0.7 kcal/mol. Actual extractions of cyclohexane-1,2-diol from buffer solutions that mimic cell lysates and suspensions in biocatalytic reactions further exemplify our findings. The yields highlight that extractions with 1-butanol can be significantly more efficient than the conventional protocol based on ethyl acetate.
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Affiliation(s)
- Gerhard König
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr , Germany.,Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr , Germany.,Department of Chemistry , Philipps-University Marburg , 35032 Marburg , Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr , Germany
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36
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Li A, Acevedo-Rocha CG, Reetz MT. Boosting the efficiency of site-saturation mutagenesis for a difficult-to-randomize gene by a two-step PCR strategy. Appl Microbiol Biotechnol 2018; 102:6095-6103. [PMID: 29785500 PMCID: PMC6013526 DOI: 10.1007/s00253-018-9041-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
Abstract
Site-saturation mutagenesis (SSM) has been used in directed evolution of proteins for a long time. As a special form of saturation mutagenesis, it involves individual randomization at a given residue with formation of all 19 amino acids. To date, the most efficient embodiment of SSM is a one-step PCR-based approach using NNK codon degeneracy. However, in the case of difficult-to-randomize genes, SSM may not deliver all of the expected 19 mutants, which compels the user to invest further efforts by applying site-directed mutagenesis for the construction of the missing mutants. To solve this problem, we developed a two-step PCR-based technique in which a mutagenic primer and a non-mutagenic (silent) primer are used to generate a short DNA fragment, which is recovered and then employed as a megaprimer to amplify the whole plasmid. The present two-step and older one-step (partially overlapped primer approach) procedures were compared by utilizing cytochrome P450-BM3, which is a "difficult-to-randomize" gene. The results document the distinct superiority of the new method by checking the library quality on DNA level based on massive sequence data, but also at amino acid level. Various future applications in biotechnology can be expected, including the utilization when constructing mutability landscapes, which provide semi-rational information for identifying hot spots for protein engineering and directed evolution.
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Affiliation(s)
- Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany.,Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | | | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany. .,Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany.
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37
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Li G, Maria-Solano MA, Romero-Rivera A, Osuna S, Reetz MT. Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution. Chem Commun (Camb) 2018; 53:9454-9457. [PMID: 28795696 DOI: 10.1039/c7cc05377k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The long-standing problem of achieving high activity of a thermophilic enzyme at low temperatures and short reaction times with little tradeoff in thermostability has been solved by directed evolution, an alcohol dehydrogenase found in hot springs serving as the catalyst in enantioselective ketone reductions.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
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Acevedo-Rocha CG, Gamble CG, Lonsdale R, Li A, Nett N, Hoebenreich S, Lingnau JB, Wirtz C, Fares C, Hinrichs H, Deege A, Mulholland AJ, Nov Y, Leys D, McLean KJ, Munro AW, Reetz MT. P450-Catalyzed Regio- and Diastereoselective Steroid Hydroxylation: Efficient Directed Evolution Enabled by Mutability Landscaping. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00389] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Charles G. Gamble
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University 368 Youyi Road, Wuchang Wuhan 430062, China
| | - Nathalie Nett
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Julia B. Lingnau
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Cornelia Wirtz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Christophe Fares
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Alfred Deege
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa 31905, Israel
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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Li A, Acevedo-Rocha CG, Sun Z, Cox T, Xu JL, Reetz MT. Front Cover: Beating Bias in the Directed Evolution of Proteins: Combining High-Fidelity on-Chip Solid-Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction (ChemBioChem 3/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aitao Li
- Department of Synthetic Organic Chemistry; Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-Universität Marburg; 35032 Marburg Germany
- Hubei Collaborative Innovation Center for, Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; College of Life Sciences; Hubei University; 368 Youyi Road Wuchang Wuhan 430062 P.R. China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Tony Cox
- Twist Bioscience; 455 Mission Bay Boulevard South San Francisco CA 94158 USA
| | - Jia Lucy Xu
- Twist Bioscience; 455 Mission Bay Boulevard South San Francisco CA 94158 USA
| | - Manfred T. Reetz
- Department of Synthetic Organic Chemistry; Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-Universität Marburg; 35032 Marburg Germany
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Ilie A, Harms K, Reetz MT. P450-Catalyzed Regio- and Stereoselective Oxidative Hydroxylation of 6-Iodotetralone: Preparative-Scale Synthesis of a Key Intermediate for Pd-Catalyzed Transformations. J Org Chem 2018; 83:7504-7508. [DOI: 10.1021/acs.joc.7b02878] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Adriana Ilie
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Str. 4, 35032 Marburg, Germany
| | - Klaus Harms
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Str. 4, 35032 Marburg, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Str. 4, 35032 Marburg, Germany
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41
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Qu G, Lonsdale R, Yao P, Li G, Liu B, Reetz MT, Sun Z. Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis. Chembiochem 2018; 19:239-246. [PMID: 29314451 DOI: 10.1002/cbic.201700562] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Peiyuan Yao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
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Abstract
Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany.
- Biosyntia ApS, 2100, Copenhagen, Denmark.
| | - Matteo Ferla
- Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany
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Li A, Acevedo-Rocha CG, Sun Z, Cox T, Xu JL, Reetz MT. Beating Bias in the Directed Evolution of Proteins: Combining High-Fidelity on-Chip Solid-Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction. Chembiochem 2017; 19:221-228. [DOI: 10.1002/cbic.201700540] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Aitao Li
- Department of Synthetic Organic Chemistry; Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-Universität Marburg; 35032 Marburg Germany
- Hubei Collaborative Innovation Center for, Green Transformation of Bio-Resources; Hubei Key Laboratory of Industrial Biotechnology; College of Life Sciences; Hubei University; 368 Youyi Road Wuchang Wuhan 430062 P.R. China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 P.R. China
| | - Tony Cox
- Twist Bioscience; 455 Mission Bay Boulevard South San Francisco CA 94158 USA
| | - Jia Lucy Xu
- Twist Bioscience; 455 Mission Bay Boulevard South San Francisco CA 94158 USA
| | - Manfred T. Reetz
- Department of Synthetic Organic Chemistry; Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-Universität Marburg; 35032 Marburg Germany
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Sun Z, Wu L, Bocola M, Chan HCS, Lonsdale R, Kong XD, Yuan S, Zhou J, Reetz MT. Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations. J Am Chem Soc 2017; 140:310-318. [DOI: 10.1021/jacs.7b10278] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Lian Wu
- State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marco Bocola
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - H. C. Stephen Chan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Xu-Dong Kong
- State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shuguang Yuan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Jiahai Zhou
- State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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Wang JB, Ilie A, Yuan S, Reetz MT. Correction to “Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe”. J Am Chem Soc 2017; 139:16996. [DOI: 10.1021/jacs.7b11564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-University; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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47
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Wang JB, Ilie A, Yuan S, Reetz MT. Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe. J Am Chem Soc 2017; 139:11241-11247. [DOI: 10.1021/jacs.7b06019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jian-bo Wang
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adriana Ilie
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Shuguang Yuan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Manfred T. Reetz
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
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48
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Li G, Yao P, Gong R, Li J, Liu P, Lonsdale R, Wu Q, Lin J, Zhu D, Reetz MT. Correction: Simultaneous engineering of an enzyme's entrance tunnel and active site: the case of monoamine oxidase MAO-N. Chem Sci 2017; 8:4666. [PMID: 30124672 PMCID: PMC6063156 DOI: 10.1039/c7sc90029e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘Simultaneous engineering of an enzyme’s entrance tunnel and active site: the case of monoamine oxidase MAO-N’ by Guangyue Li et al., Chem. Sci., 2017, 8, 4093–4099.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany . .,Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse, Marburg , 35032 , Germany
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Rui Gong
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Jinlong Li
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Pi Liu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany . .,Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse, Marburg , 35032 , Germany
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Jianping Lin
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China .
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany . .,Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse, Marburg , 35032 , Germany
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49
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Wang JB, Ilie A, Reetz MT. Chemo- and Stereoselective Cytochrome P450-BM3-Catalyzed Sulfoxidation of 1-Thiochroman-4-ones Enabled by Directed Evolution. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700414] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jian-bo Wang
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim/Ruhr Germany
- Fachbereich Chemie, Philipps-Universität; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Adriana Ilie
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim/Ruhr Germany
- Fachbereich Chemie, Philipps-Universität; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim/Ruhr Germany
- Fachbereich Chemie, Philipps-Universität; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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50
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Li G, Yao P, Gong R, Li J, Liu P, Lonsdale R, Wu Q, Lin J, Zhu D, Reetz MT. Simultaneous engineering of an enzyme's entrance tunnel and active site: the case of monoamine oxidase MAO-N. Chem Sci 2017; 8:4093-4099. [PMID: 30155214 PMCID: PMC6099926 DOI: 10.1039/c6sc05381e] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
A new directed evolution approach is presented to enhance the activity of an enzyme and to manipulate stereoselectivity by focusing iterative saturation mutagenesis (ISM) simultaneously on residues lining the entrance tunnel and the binding pocket. This combined mutagenesis strategy was applied successfully to the monoamine oxidase from Aspergillus niger (MAO-N) in the reaction of sterically demanding substrates which are of interest in the synthesis of chiral pharmaceuticals based on the benzo-piperidine scaffold. Reversal of enantioselectivity of Turner-type deracemization was achieved in the synthesis of (S)-1,2,3,4-tetrahydro-1-methyl-isoquinoline, (S)-1,2,3,4-tetrahydro-1-ethylisoquinoline and (S)-1,2,3,4-tetrahydro-1-isopropylisoquinoline. Extensive molecular dynamics simulations indicate that the altered catalytic profile is due to increased hydrophobicity of the entrance tunnel acting in concert with the altered shape of the binding pocket.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Rui Gong
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Jinlong Li
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Pi Liu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Jianping Lin
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes , Tianjin Engineering Center for Biocatalytic Technology , Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , 32 Xi Qi Dao, Tianjin Airport Economic Area , Tianjin 300308 , People's Republic of China . ;
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany .
- Fachbereich Chemie , Philipps-Universität , Hans-Meerwein-Strasse , 35032 Marburg , Germany
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