1
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Wu X, Zhou L, Li F, Xiao J. PCl 3-mediated transesterification and aminolysis of tert-butyl esters via acid chloride formation. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/1747519820987530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A PCl3-mediated conversion of tert-butyl esters into esters and amides in one-pot under air is developed. This novel protocol is highlighted by the synthesis of skeletons of bioactive molecules and gram-scale reactions. Mechanistic studies revealed that this transformation involves the formation of an acid chloride in situ, which is followed by reactions with alcohols or amines to afford the desired products.
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Affiliation(s)
- Xiaofang Wu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, P.R. China
| | - Lei Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, P.R. China
| | - Fangshao Li
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, P.R. China
| | - Jing Xiao
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, P.R. China
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2
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Biler M, Crean RM, Schweiger AK, Kourist R, Kamerlin SCL. Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase. J Am Chem Soc 2020; 142:20216-20231. [PMID: 33180505 PMCID: PMC7735706 DOI: 10.1021/jacs.0c10701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity, and selectivity of this enzyme are only poorly understood to date, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the nonconverted or poorly converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering.
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Affiliation(s)
- Michal Biler
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Rory M. Crean
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Anna K. Schweiger
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
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3
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Dasgupta S, Herbert JM. Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites. J Phys Chem B 2020; 124:1137-1147. [PMID: 31986049 DOI: 10.1021/acs.jpcb.9b11060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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4
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Enoki J, Mügge C, Tischler D, Miyamoto K, Kourist R. Chemoenzymatic Cascade Synthesis of Optically Pure Alkanoic Acids by Using Engineered Arylmalonate Decarboxylase Variants. Chemistry 2019; 25:5071-5076. [PMID: 30702787 PMCID: PMC6563808 DOI: 10.1002/chem.201806339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 11/09/2022]
Abstract
Arylmalonate decarboxylase (AMDase) catalyzes the cofactor‐free asymmetric decarboxylation of prochiral arylmalonic acids and produces the corresponding monoacids with rigorous R selectivity. Alteration of catalytic cysteine residues and of the hydrophobic environment in the active site by protein engineering has previously resulted in the generation of variants with opposite enantioselectivity and improved catalytic performance. The substrate spectrum of AMDase allows it to catalyze the asymmetric decarboxylation of small methylvinylmalonic acid derivatives, implying the possibility to produce short‐chain 2‐methylalkanoic acids with high optical purity after reduction of the nonactivated C=C double bond. Use of diimide as the reductant proved to be a simple strategy to avoid racemization of the stereocenter during reduction. The developed chemoenzymatic sequential cascade with use of R‐ and S‐selective AMDase variants produced optically pure short‐chain 2‐methylalkanoic acids in moderate to full conversion and gave both enantiomers in excellent enantiopurity (up to 83 % isolated yield and 98 % ee).
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Affiliation(s)
- Junichi Enoki
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitätstraße 150, 44780, Bochum, Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitätstraße 150, 44780, Bochum, Germany
| | - Dirk Tischler
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitätstraße 150, 44780, Bochum, Germany
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 22308522, Yokohama, Japan
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
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5
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Kar D, Pandey SD, Mallick S, Dutta M, Ghosh AS. Substitution of Alanine at Position 184 with Glutamic Acid in Escherichia coli PBP5 Ω-Like Loop Introduces a Moderate Cephalosporinase Activity. Protein J 2018; 37:122-131. [DOI: 10.1007/s10930-018-9765-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Cofactor engineering in cyanobacteria to overcome imbalance between NADPH and NADH: A mini review. Front Chem Sci Eng 2017. [DOI: 10.1007/s11705-016-1591-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Karmakar T, Balasubramanian S. Molecular Dynamics and Free Energy Simulations of Phenylacetate and CO 2 Release from AMDase and Its G74C/C188S Mutant: A Possible Rationale for the Reduced Activity of the Latter. J Phys Chem B 2016; 120:11644-11653. [PMID: 27775347 DOI: 10.1021/acs.jpcb.6b07034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arylmalonate decarboxylase (AMDase) catalyzes the decarboxylation of α-aryl-α-methyl malonates to produce optically pure α-arylpropionates of industrial and medicinal importance. Herein, atomistic molecular dynamics simulations have been carried out to delineate the mechanism of the release of product molecules phenylacetate (PAC) and carbon dioxide (CO2), from the wild-type (WT) and its G74C/C188S mutant enzymes. Both of the product molecules follow a crystallographically characterized solvent-accessible channel to come out of the protein interior. A higher free energy barrier for the release of PAC from G74C/C188S compared to that in the WT is consistent with the experimentally observed compromised efficiency of the mutant. The release of CO2 precedes that of PAC; free energy barriers for CO2 and PAC release in the WT enzyme are calculated to be ∼1-2 and ∼23 kcal/mol, respectively. Postdecarboxylation, CO2 moves toward a hydrophobic pocket formed by Pro 14, Leu 38, Leu 40, Leu 77, and the side chain of Tyr 48 which serves as its temporary "reservoir". CO2 releases following a channel mainly decorated by apolar residues, unlike in the case of oxalate decarboxylase where polar residues mediate its transport.
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Affiliation(s)
- Tarak Karmakar
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
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8
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Miyamoto K, Kourist R. Arylmalonate decarboxylase—a highly selective bacterial biocatalyst with unknown function. Appl Microbiol Biotechnol 2016; 100:8621-31. [PMID: 27566691 DOI: 10.1007/s00253-016-7778-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/27/2016] [Accepted: 08/02/2016] [Indexed: 11/24/2022]
Affiliation(s)
- Kenji Miyamoto
- Department for Biosciences and Bioinformatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, 44780, Bochum, Germany.
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9
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Gaßmeyer SK, Wetzig J, Mügge C, Assmann M, Enoki J, Hilterhaus L, Zuhse R, Miyamoto K, Liese A, Kourist R. Arylmalonate Decarboxylase-Catalyzed Asymmetric Synthesis of Both Enantiomers of Optically Pure Flurbiprofen. ChemCatChem 2016. [DOI: 10.1002/cctc.201501205] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Jasmin Wetzig
- Chiracon GmbH; Im Biotechnologiepark 14943 Luckenwalde Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology; Ruhr-University Bochum; 44780 Bochum Germany
| | - Miriam Assmann
- Institute for Technical Biocatalysis; Hamburg University of Technology TUHH; Denickestr. 15 21071 Hamburg Germany
| | - Junichi Enoki
- Junior Research Group for Microbial Biotechnology; Ruhr-University Bochum; 44780 Bochum Germany
| | - Lutz Hilterhaus
- Institute for Technical Biocatalysis; Hamburg University of Technology TUHH; Denickestr. 15 21071 Hamburg Germany
| | - Ralf Zuhse
- Chiracon GmbH; Im Biotechnologiepark 14943 Luckenwalde Germany
| | - Kenji Miyamoto
- Department for Biosciences and Bioinformatics; Keio University; 3-14-1 Hiyoshi Yokohama 223-8522 Japan
| | - Andreas Liese
- Institute for Technical Biocatalysis; Hamburg University of Technology TUHH; Denickestr. 15 21071 Hamburg Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology; Ruhr-University Bochum; 44780 Bochum Germany
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10
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Busch F, Enoki J, Hülsemann N, Miyamoto K, Bocola M, Kourist R. Semiempirical QM/MM calculations reveal a step-wise proton transfer and an unusual thiolate pocket in the mechanism of the unique arylpropionate racemase AMDase G74C. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01964h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Semiempirical calculations on the mechanism of the arylpropionate racemase AMDase G74C reveal a step-wise mechanism involving a planar-enedionate intermediate.
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Affiliation(s)
- F. Busch
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
| | - J. Enoki
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
| | - N. Hülsemann
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
| | - K. Miyamoto
- Department of Bioscience and Informatics
- Keio University
- Yokohama
- Japan
| | - M. Bocola
- Institute of Biotechnology
- RWTH Aachen
- 52062 Aachen
- Germany
| | - R. Kourist
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
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11
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Gaßmeyer SK, Yoshikawa H, Enoki J, Hülsemann N, Stoll R, Miyamoto K, Kourist R. STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C. Chembiochem 2015; 16:1943-1949. [DOI: 10.1002/cbic.201500253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 02/01/2023]
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12
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Lind MES, Himo F. Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase. ACS Catal 2014. [DOI: 10.1021/cs5009738] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maria E. S. Lind
- Department
of Organic Chemistry
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department
of Organic Chemistry
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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13
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Kourist R, Guterl JK, Miyamoto K, Sieber V. Enzymatic Decarboxylation-An Emerging Reaction for Chemicals Production from Renewable Resources. ChemCatChem 2014. [DOI: 10.1002/cctc.201300881] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angew Chem Int Ed Engl 2013; 52:5700-25. [PMID: 23526810 DOI: 10.1002/anie.201204077] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 11/07/2022]
Abstract
Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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15
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computerbasiertes Enzymdesign. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Steiner K, Schwab H. Recent advances in rational approaches for enzyme engineering. Comput Struct Biotechnol J 2012; 2:e201209010. [PMID: 24688651 PMCID: PMC3962183 DOI: 10.5936/csbj.201209010] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 11/29/2022] Open
Abstract
Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks. To meet the requirements of industrial biotechnology and to introduce new functionalities, the enzymes need to be optimized by protein engineering. This article specifically reviews rational approaches for enzyme engineering and de novo enzyme design involving structure-based approaches developed in recent years for improvement of the enzymes’ performance, broadened substrate range, and creation of novel functionalities to obtain products with high added value for industrial applications.
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Affiliation(s)
- Kerstin Steiner
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria ; Institute of Molecular Biotechnology, TU Graz, 8010 Graz, Austria
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17
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Gröger H, Asano Y, Bornscheuer UT, Ogawa J. Development of biocatalytic processes in Japan and Germany: from research synergies to industrial applications. Chem Asian J 2012; 7:1138-53. [PMID: 22550022 DOI: 10.1002/asia.201200105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Harald Gröger
- Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany.
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18
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Li T, Huo L, Pulley C, Liu A. Decarboxylation mechanisms in biological system. Bioorg Chem 2012; 43:2-14. [PMID: 22534166 DOI: 10.1016/j.bioorg.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/04/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
Abstract
This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.
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Affiliation(s)
- Tingfeng Li
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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19
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Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol 2012; 8:294-300. [PMID: 22306579 DOI: 10.1038/nchembio.777] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/25/2011] [Indexed: 11/08/2022]
Abstract
The ability to redesign enzymes to catalyze noncognate chemical transformations would have wide-ranging applications. We developed a computational method for repurposing the reactivity of metalloenzyme active site functional groups to catalyze new reactions. Using this method, we engineered a zinc-containing mouse adenosine deaminase to catalyze the hydrolysis of a model organophosphate with a catalytic efficiency (k(cat)/K(m)) of ~10(4) M(-1) s(-1) after directed evolution. In the high-resolution crystal structure of the enzyme, all but one of the designed residues adopt the designed conformation. The designed enzyme efficiently catalyzes the hydrolysis of the R(P) isomer of a coumarinyl analog of the nerve agent cyclosarin, and it shows marked substrate selectivity for coumarinyl leaving groups. Computational redesign of native enzyme active sites complements directed evolution methods and offers a general approach for exploring their untapped catalytic potential for new reactivities.
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20
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Ema T, Nakano Y, Yoshida D, Kamata S, Sakai T. Redesign of enzyme for improving catalytic activity and enantioselectivity toward poor substrates: manipulation of the transition state. Org Biomol Chem 2012; 10:6299-308. [DOI: 10.1039/c2ob25614b] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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21
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Bornscheuer U, Kazlauskas RJ. Survey of protein engineering strategies. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 26:26.7.1-26.7.14. [PMID: 22045562 DOI: 10.1002/0471140864.ps2607s66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein engineering is altering the structure of a protein to improve or change its properties. This unit summarizes concepts for protein engineering using rational design, directed evolution, and combinations of them. Different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are given. This should enable researchers to choose the most promising tools to solve their protein engineering challenges.
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Affiliation(s)
- Uwe Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
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22
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Affiliation(s)
- Maria Svedendahl Humble
- Division of Biochemistry, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, 10691 Stockholm, Sweden, Fax: +46‐8‐5537‐8468
| | - Per Berglund
- Division of Biochemistry, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, 10691 Stockholm, Sweden, Fax: +46‐8‐5537‐8468
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23
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Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M. Application of Designed Enzymes in Organic Synthesis. Chem Rev 2011; 111:4141-64. [DOI: 10.1021/cr100386u] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gernot A. Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Oliver May
- DSM—Innovative Synthesis BV, Geleen, P.O. Box 18, 6160 MD Geleen, The Netherlands
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24
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Jochens H, Hesseler M, Stiba K, Padhi SK, Kazlauskas RJ, Bornscheuer UT. Protein Engineering of α/β-Hydrolase Fold Enzymes. Chembiochem 2011; 12:1508-17. [DOI: 10.1002/cbic.201000771] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Indexed: 01/01/2023]
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25
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Padhi SK, Fujii R, Legatt GA, Fossum SL, Berchtold R, Kazlauskas RJ. Switching from an esterase to a hydroxynitrile lyase mechanism requires only two amino acid substitutions. ACTA ACUST UNITED AC 2011; 17:863-71. [PMID: 20797615 DOI: 10.1016/j.chembiol.2010.06.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 05/16/2010] [Accepted: 06/01/2010] [Indexed: 11/16/2022]
Abstract
The alpha/beta hydrolase superfamily contains mainly esterases, which catalyze hydrolysis, but also includes hydroxynitrile lyases, which catalyze addition of cyanide to aldehydes, a carbon-carbon bond formation. Here, we convert a plant esterase, SABP2, into a hydroxynitrile lyase using just two amino acid substitutions. Variant SABP2-G12T-M239K lost the ability to catalyze ester hydrolysis (<0.9 mU/mg) and gained the ability to catalyze the release of cyanide from mandelonitrile (20 mU/mg, k(cat)/K(M) = 70 min(-1)M(-1)). This variant also catalyzed the reverse reaction, formation of mandelonitrile with low enantioselectivity: 20% ee (S), E = 1.5. The specificity constant for the lysis of mandelontrile is 13,000-fold faster than the uncatalyzed reaction and only 1300-fold less efficient (k(cat/)K(M)) than hydroxynitrile lyase from rubber tree.
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Affiliation(s)
- Santosh Kumar Padhi
- Department of Biochemistry, Molecular Biology, and Biophysics, and the Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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Kourist R, Miyauchi Y, Uemura D, Miyamoto K. Engineering the promiscuous racemase activity of an arylmalonate decarboxylase. Chemistry 2010; 17:557-63. [PMID: 21207573 DOI: 10.1002/chem.201001924] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Indexed: 11/06/2022]
Abstract
Variant G74C of arylmalonate decarboxylase (AMDase) from Bordatella bronchoseptica has a unique racemising activity towards profens. By protein engineering, variant G74C/V43A with a 20-fold shift towards promiscuous racemisation was obtained, based on a reduced activity in the decarboxylation reaction and a two-fold increase in the racemisation activity. The mutant showed an extended substrate range, with a 30-fold increase in the reaction rate towards ketoprofen. Molecular dynamics simulations and the substrate profile of the racemase indicate that the steric and polar effects of the substrate structure play a more dominant role on catalysis than mere kinetic α-proton acidity. The observation that the conversion of β,γ-unsaturated carboxylic acids does not lead to a rearrangement to form their α,β isomers indicates a concerted rather than a stepwise mechanism. Interestingly, a substrate bearing a nitro group instead of the carboxylic acid group on the α-carbon atom was also converted by the racemase.
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Affiliation(s)
- Robert Kourist
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522 Yokohama, Japan
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Obata R, Nakasako M. Structural basis for inverting the enantioselectivity of arylmalonate decarboxylase revealed by the structural analysis of the Gly74Cys/Cys188Ser mutant in the liganded form. Biochemistry 2010; 49:1963-9. [PMID: 20136121 DOI: 10.1021/bi9015605] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arylmalonate decarboxylase catalyzes the enantioselective decarboxylation of alpha-aryl-alpha-methylmalonate to produce optically pure alpha-arylpropionate. The enzyme is comprised of two alpha/beta domains and contains an active site situated between the two domains. The site is formed by Tyr48, Gly74-Thr75-Ser76, Tyr126, and Cys188-Gly189-Gly190 residues. Since it has been observed that the Gly74Cys/Cys188Ser mutation inverts the enantioselectivity of the enzyme, we determined the crystal structure of the Gly74Cys/Cys188Ser mutant in the liganded form at a resolution of 1.45 A to understand the structural basis for this inversion. The overall structure of the enzyme overlapped well with that of the benzylphosphonate-associated wild-type enzyme, and the mutations had little effect on the structure of the active site. A ligand molecule bound to the active site in an unusual semiplanar conformation resembling the planar enediolate reaction intermediate could be assigned as phenyl acetate. The inversion in enantioselectivity by the paired mutation is explained by the mirror symmetry between Cys74 in the mutant and Cys188 of the wild type with respect to the carbon atom in the ligand to be protonated. Comparison of the wild-type and Gly74Cys mutant crystal structures suggested that ligand binding induces a positional shift of the Cys188-Gly189-Gly190 region toward the Gly74-Thr75 pair which provides two oxyanion holes necessary to stabilize the negatively charged enediolate reaction intermediate. The ligand binding also simultaneously induces the formation of a hydrophobic cluster over the active site cleft. Thus, AMDase is proposed to have "open" and "closed" conformations of the active site that are regulated by ligand binding. These results may provide an effective strategy for the rational design to invert the enantioselectivity of enzymes.
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Affiliation(s)
- Rika Obata
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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Ema T, Kamata S, Takeda M, Nakano Y, Sakai T. Rational creation of mutant enzyme showing remarkable enhancement of catalytic activity and enantioselectivity toward poor substrates. Chem Commun (Camb) 2010; 46:5440-2. [DOI: 10.1039/c001561j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Matsui T, Kato K, Namihira T, Shinzato N, Semba H. Stereospecific degradation of phenylsuccinate by actinomycetes. CHEMOSPHERE 2009; 76:1278-1282. [PMID: 19580991 DOI: 10.1016/j.chemosphere.2009.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 06/05/2009] [Accepted: 06/05/2009] [Indexed: 05/28/2023]
Abstract
Racemic phenylsuccinate was stereospecifically degraded by the actinomycetes PS9 and PS17 isolated from soil obtained from Okinawa Island, Japan. Strain PS9, identified as a Citricoccus sp., preferentially degraded the R-form, while strain PS17, identified as a Microbacterium sp., preferentially degraded the S-form of phenylsuccinate. Analysis of the culture broths of these species with phenylsuccinate as the sole carbon source revealed that benzoic acid was produced as a metabolic intermediate. Benzoic acid was further degraded by strain PS9 with m- and/or p-hydroxybenzoic acid but not o-hydroxybenzoic acid as possible intermediates.
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Affiliation(s)
- Toru Matsui
- Center of Molecular Biosciences, University of the Ryukyus, 1 Sembaru, Nishihara-cho, Okinawa 903-0213, Japan.
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Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas R, Bornscheuer U. Umwandlung einer Esterase in eine Epoxidhydrolase. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas R, Bornscheuer U. Converting an Esterase into an Epoxide Hydrolase. Angew Chem Int Ed Engl 2009; 48:3532-5. [DOI: 10.1002/anie.200806276] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gerlt JA, Babbitt PC. Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol 2009; 13:10-8. [PMID: 19237310 DOI: 10.1016/j.cbpa.2009.01.014] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 01/14/2009] [Indexed: 11/15/2022]
Abstract
The (re)design of enzymes to catalyze 'new' reactions is a topic of considerable practical and intellectual interest. Directed evolution (random mutagenesis followed by screening/selection) has been used widely to identify novel biocatalysts. However, 'rational' approaches using either natural divergent evolution or computational predictions based on chemical principles have been less successful. This review summarizes recent progress in evolution-based and computation-based (re)design.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, University of Illinois, Urbana, 61801, United States.
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Asymmetric Malonic and Acetoacetic Acid Syntheses – A Century of Enantioselective Decarboxylative Protonations. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800759] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Okrasa K, Levy C, Hauer B, Baudendistel N, Leys D, Micklefield J. Structure and Mechanism of an Unusual Malonate Decarboxylase and Related Racemases. Chemistry 2008; 14:6609-13. [DOI: 10.1002/chem.200800918] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Nakasako M, Obata R, Okubo R, Nakayama S, Miyamoto K, Ohta H. Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:610-3. [PMID: 18607088 DOI: 10.1107/s1744309108014723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 05/15/2008] [Indexed: 11/11/2022]
Abstract
Arylmalonate decarboxylase catalyses the enantioselective decarboxylation of alpha-aryl-alpha-methylmalonates to produce optically pure alpha-arylpropionates. The enzyme was crystallized with ammonium sulfate under alkaline pH conditions with the aim of understanding the mechanism of the enantioselective reaction. X-ray diffraction data collected to a resolution of 3.0 A at cryogenic temperature showed that the crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 83.13, b = 99.62, c = 139.64 A. This suggested that the asymmetric unit would contain between four and six molecules. Small-angle X-ray scattering revealed that the enzyme exists as a monomer in solution. Thus, the assembly of molecules in the asymmetric unit was likely to have been induced during the crystallization process.
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Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522, Japan.
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Active-Site Mobility Revealed by the Crystal Structure of Arylmalonate Decarboxylase from Bordetella bronchiseptica. J Mol Biol 2008; 377:386-94. [DOI: 10.1016/j.jmb.2007.12.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/18/2007] [Accepted: 12/26/2007] [Indexed: 11/19/2022]
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Terao Y, Miyamoto K, Ohta H. The Aldol Type Reaction Catalyzed by Arylmalonate Decarboxylase —A Decarboxylase can Catalyze an Entirely Different Reaction, Aldol Reaction—. CHEM LETT 2007. [DOI: 10.1246/cl.2007.420] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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