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Peroxyacetic Acid Pretreatment: A Potentially Promising Strategy towards Lignocellulose Biorefinery. Molecules 2022; 27:molecules27196359. [PMID: 36234896 PMCID: PMC9573572 DOI: 10.3390/molecules27196359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
The stubborn and complex structure of lignocellulose hinders the valorization of each component of cellulose, hemicellulose, and lignin in the biorefinery industries. Therefore, efficient pretreatment is an essential and prerequisite step for lignocellulose biorefinery. Recently, a considerable number of studies have focused on peroxyacetic acid (PAA) pretreatment in lignocellulose fractionation and some breakthroughs have been achieved in recent decades. In this article, we aim to highlight the challenges of PAA pretreatment and propose a roadmap towards lignocellulose fractionation by PAA for future research. As a novel promising pretreatment method towards lignocellulosic fractionation, PAA is a strong oxidizing agent that can selectively remove lignin and hemicellulose from lignocellulose, retaining intact cellulose for downstream upgrading. PAA in lignocellulose pretreatment can be divided into commercial PAA, chemical activation PAA, and enzymatic in-situ generation of PAA. Each PAA for lignocellulose fractionation shows its own advantages and disadvantages. To meet the theme of green chemistry, enzymatic in-situ generation of PAA has aroused a great deal of enthusiasm in lignocellulose fractionation. Furthermore, mass balance and techno-economic analyses are discussed in order to evaluate the feasibility of PAA pretreatment in lignocellulose fractionation. Ultimately, some perspectives and opportunities are proposed to address the existing limitations in PAA pretreatment towards biomass biorefinery valorization. In summary, from the views of green chemistry, enzymatic in-situ generation of PAA will become a cutting-edge topic research in the lignocellulose fractionation in future.
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2
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Salmi T, Aguilera AF, Lindroos P, Kanerva L. Mathematical modelling of oleic acid epoxidation via a chemo-enzymatic route – From reaction mechanisms to reactor model. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Facile fabrication of antibacterial and antiviral perhydrolase-polydopamine composite coatings. Sci Rep 2021; 11:12410. [PMID: 34127732 PMCID: PMC8203652 DOI: 10.1038/s41598-021-91925-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/31/2021] [Indexed: 01/03/2023] Open
Abstract
In situ generation of antibacterial and antiviral agents by harnessing the catalytic activity of enzymes on surfaces provides an effective eco-friendly approach for disinfection. The perhydrolase (AcT) from Mycobacterium smegmatis catalyzes the perhydrolysis of acetate esters to generate the potent disinfectant, peracetic acid (PAA). In the presence of AcT and its two substrates, propylene glycol diacetate and H2O2, sufficient and continuous PAA is generated over an extended time to kill a wide range of bacteria with the enzyme dissolved in aqueous buffer. For extended self-disinfection, however, active and stable AcT bound onto or incorporated into a surface coating is necessary. In the current study, an active, stable and reusable AcT-based coating was developed by incorporating AcT into a polydopamine (PDA) matrix in a single step, thereby forming a biocatalytic composite onto a variety of surfaces. The resulting AcT-PDA composite coatings on glass, metal and epoxy surfaces yielded up to 7-log reduction of Gram-positive and Gram-negative bacteria when in contact with the biocatalytic coating. This composite coating also possessed potent antiviral activity, and dramatically reduced the infectivity of a SARS-CoV-2 pseudovirus within minutes. The single-step approach enables rapid and facile fabrication of enzyme-based disinfectant composite coatings with high activity and stability, which enables reuse following surface washing. As a result, this enzyme-polymer composite technique may serve as a general strategy for preparing antibacterial and antiviral surfaces for applications in health care and common infrastructure safety, such as in schools, the workplace, transportation, etc.
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Su W, Li Q, Liu Y, Qin Y, Liu H, Tang A. Improved efficiency of lipase-mediated epoxidation of α-pinene using H2O2 in single-phase systems. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Jia W, Li H, Wang Q, Zheng K, Lin H, Li X, Huang J, Xu L, Dong W, Shu Z. Screening of perhydrolases to optimize glucose oxidase-perhydrolase-in situ chemical oxidation cascade reaction system and its application in melanin decolorization. J Biotechnol 2021; 328:106-114. [PMID: 33485863 DOI: 10.1016/j.jbiotec.2021.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/02/2021] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
A novel glucose oxidase (GOD)-perhydrolase-in situ chemical oxidation (ISCO) cascade reaction system was designed, optimized, and verified the operation feasibility in this research. Among the determined four perhydrolases, acyltransferase from Mycobacterium smegmatis (MsAcT) displayed the highest specific activity for perhydrolysis reaction (76.4 U/mg) and the lowest Km value to hydrogen peroxide (13.9 mmol/L). GOD-MsAcT cascade reaction system also displayed high catalytic efficiency. Under the optimal parameters (50:1 activity unit ratio of GOD to MsAcT, pH 8.0, 50 mmol/L of β-d-glucose, and 15 mmol/L of glyceryl triacetate), the melanin decolorization rate using GOD-MsAcT-ISCO cascade reaction system reached 86.8 %. Kinetics of GOD-MsAcT-ISCO cascade reaction system for melanin decolorization fitted the kinetic model of Boltzmann sigmoid. As a substitutive skin whitening technology, GOD-MsAcT-ISCO cascade reaction system displayed an excellent application prospect.
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Affiliation(s)
- Wenjing Jia
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Huan Li
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Qian Wang
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Kaixuan Zheng
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China; Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Fujian Normal University, Fuzhou, 350117, China
| | - Hong Lin
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Xin Li
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Jianzhong Huang
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China.
| | - Linting Xu
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Wanqian Dong
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China
| | - Zhengyu Shu
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technology, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China; College of Life Sciences, Fujian Normal University (Qishan Campus), Fuzhou, 350117, China; Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Fujian Normal University, Fuzhou, 350117, China.
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6
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Zhang T, Ma Y, Tan CP, Hollmann F, Wang J, Yang B, Wang Y. An Efficient Strategy for the Production of Epoxidized Oils: Natural Deep Eutectic Solvent‐Based Enzymatic Epoxidation. J AM OIL CHEM SOC 2019. [DOI: 10.1002/aocs.12220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tianyu Zhang
- School of Bioscience and BioengineeringSouth China University of Technology, No.382, East Waihuan Guangzhou, 510006 China
| | - Yunjian Ma
- School of Food Science and EngineeringSouth China University of Technology, No.381, Wushan Guangzhou, 510640 China
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and TechnologyUniversiti Putra Malaysia, High‐tech Industrial Park 43400, Serdang Selangor Malaysia
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9, 2629HZ, Delft The Netherlands
| | - Jianrong Wang
- School of Bioscience and BioengineeringSouth China University of Technology, No.382, East Waihuan Guangzhou, 510006 China
| | - Bo Yang
- School of Bioscience and BioengineeringSouth China University of Technology, No.382, East Waihuan Guangzhou, 510006 China
| | - Yonghua Wang
- School of Food Science and EngineeringSouth China University of Technology, No.381, Wushan Guangzhou, 510640 China
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7
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Dynamic kinetic resolution of Vince lactam catalyzed by γ-lactamases: a mini-review. ACTA ACUST UNITED AC 2018; 45:1017-1031. [DOI: 10.1007/s10295-018-2093-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 10/28/2022]
Abstract
Abstract
γ-Lactamases are versatile enzymes used for enzymatic kinetic resolution of racemic Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) in the industry. Optically pure enantiomers and their hydrolytic products are widely employed as key chemical intermediates for developing a wide range of carbocyclic nucleoside medicines, including US FDA-approved drugs peramivir and abacavir. Owing to the broad applications in the healthcare industry, the resolution process of Vince lactam has witnessed tremendous progress during the past decades. Some of the most important advances are the enzymatic strategies involving γ-lactamases. The strong industrial demand drives the progress in various strategies for discovering novel biocatalysts. In the past few years, several new scientific breakthroughs, including the genome-mining strategy and elucidation of several crystal structures, boosted the research on γ-lactamases. So far, several families of γ-lactamases for resolution of Vince lactam have been discovered, and their number is continuously increasing. The purpose of this mini-review is to describe the discovery strategy and classification of these intriguing enzymes and to cover our current knowledge on their potential biological functions. Moreover, structural properties are described in addition to their possible catalytic mechanisms. Additionally, recent advances in the newest approaches, such as immobilization to increase stability, and other engineering efforts are introduced.
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Dong J, Fernández‐Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biocatalytic Oxidation Reactions: A Chemist's Perspective. Angew Chem Int Ed Engl 2018; 57:9238-9261. [PMID: 29573076 PMCID: PMC6099261 DOI: 10.1002/anie.201800343] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/25/2023]
Abstract
Oxidation chemistry using enzymes is approaching maturity and practical applicability in organic synthesis. Oxidoreductases (enzymes catalysing redox reactions) enable chemists to perform highly selective and efficient transformations ranging from simple alcohol oxidations to stereoselective halogenations of non-activated C-H bonds. For many of these reactions, no "classical" chemical counterpart is known. Hence oxidoreductases open up shorter synthesis routes based on a more direct access to the target products. The generally very mild reaction conditions may also reduce the environmental impact of biocatalytic reactions compared to classical counterparts. In this Review, we critically summarise the most important recent developments in the field of biocatalytic oxidation chemistry and identify the most pressing bottlenecks as well as promising solutions.
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Affiliation(s)
- JiaJia Dong
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Elena Fernández‐Fueyo
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Milja Pesic
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Sandy Schmidt
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Yonghua Wang
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510640P. R. China
| | - Sabry Younes
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Wuyuan Zhang
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
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Dong J, Fernández-Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biokatalytische Oxidationsreaktionen - aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800343] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- JiaJia Dong
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Elena Fernández-Fueyo
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Caroline E. Paul
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Milja Pesic
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Sandy Schmidt
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Yonghua Wang
- School of Food Science and Engineering; South China University of Technology; Guangzhou 510640 P. R. China
| | - Sabry Younes
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Wuyuan Zhang
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
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10
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Wu X, Kwon SJ, Kim J, Kane RS, Dordick JS. Biocatalytic Nanocomposites for Combating Bacterial Pathogens. Annu Rev Chem Biomol Eng 2017; 8:87-113. [DOI: 10.1146/annurev-chembioeng-060816-101612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xia Wu
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ravi S. Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Jonathan S. Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180
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11
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Zhou P, Lan D, Popowicz GM, Wang X, Yang B, Wang Y. Enhancing H2O2 resistance of an esterase from Pyrobaculum calidifontis by structure-guided engineering of the substrate binding site. Appl Microbiol Biotechnol 2017; 101:5689-5697. [DOI: 10.1007/s00253-017-8299-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/06/2017] [Accepted: 04/12/2017] [Indexed: 11/28/2022]
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12
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Littlechild JA. Improving the 'tool box' for robust industrial enzymes. J Ind Microbiol Biotechnol 2017; 44:711-720. [PMID: 28401315 PMCID: PMC5408032 DOI: 10.1007/s10295-017-1920-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/05/2017] [Indexed: 01/31/2023]
Abstract
The speed of sequencing of microbial genomes and metagenomes is providing an ever increasing resource for the identification of new robust biocatalysts with industrial applications for many different aspects of industrial biotechnology. Using 'natures catalysts' provides a sustainable approach to chemical synthesis of fine chemicals, general chemicals such as surfactants and new consumer-based materials such as biodegradable plastics. This provides a sustainable and 'green chemistry' route to chemical synthesis which generates no toxic waste and is environmentally friendly. In addition, enzymes can play important roles in other applications such as carbon dioxide capture, breakdown of food and other waste streams to provide a route to the concept of a 'circular economy' where nothing is wasted. The use of improved bioinformatic approaches and the development of new rapid enzyme activity screening methodology can provide an endless resource for new robust industrial biocatalysts.This mini-review will discuss several recent case studies where industrial enzymes of 'high priority' have been identified and characterised. It will highlight specific hydrolase enzymes and recent case studies which have been carried out within our group in Exeter.
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Affiliation(s)
- J A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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13
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Lee CW, Kwon S, Park SH, Kim BY, Yoo W, Ryu BH, Kim HW, Shin SC, Kim S, Park H, Kim TD, Lee JH. Crystal Structure and Functional Characterization of an Esterase (EaEST) from Exiguobacterium antarcticum. PLoS One 2017; 12:e0169540. [PMID: 28125606 PMCID: PMC5268438 DOI: 10.1371/journal.pone.0169540] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/19/2016] [Indexed: 11/19/2022] Open
Abstract
A novel microbial esterase, EaEST, from a psychrophilic bacterium Exiguobacterium antarcticum B7, was identified and characterized. To our knowledge, this is the first report describing structural analysis and biochemical characterization of an esterase isolated from the genus Exiguobacterium. Crystal structure of EaEST, determined at a resolution of 1.9 Å, showed that the enzyme has a canonical α/β hydrolase fold with an α-helical cap domain and a catalytic triad consisting of Ser96, Asp220, and His248. Interestingly, the active site of the structure of EaEST is occupied by a peracetate molecule, which is the product of perhydrolysis of acetate. This result suggests that EaEST may have perhydrolase activity. The activity assay showed that EaEST has significant perhydrolase and esterase activity with respect to short-chain p-nitrophenyl esters (≤C8), naphthyl derivatives, phenyl acetate, and glyceryl tributyrate. However, the S96A single mutant had low esterase and perhydrolase activity. Moreover, the L27A mutant showed low levels of protein expression and solubility as well as preference for different substrates. On conducting an enantioselectivity analysis using R- and S-methyl-3-hydroxy-2-methylpropionate, a preference for R-enantiomers was observed. Surprisingly, immobilized EaEST was found to not only retain 200% of its initial activity after incubation for 1 h at 80°C, but also retained more than 60% of its initial activity after 20 cycles of reutilization. This research will serve as basis for future engineering of this esterase for biotechnological and industrial applications.
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Affiliation(s)
- Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Sena Kwon
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Boo-Young Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Han-Woo Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Seung Chul Shin
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Sunghwan Kim
- New Drug Development Center, Daegu-Gyeongpuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - T. Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
- * E-mail: (JHL); (TDK)
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
- * E-mail: (JHL); (TDK)
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14
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Zhou P, Wang X, Yang B, Hollmann F, Wang Y. Chemoenzymatic epoxidation of alkenes with Candida antarctica lipase B and hydrogen peroxide in deep eutectic solvents. RSC Adv 2017. [DOI: 10.1039/c7ra00805h] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Epoxides are important synthetic intermediates for the synthesis of a broad range of industrial products.
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Affiliation(s)
- Pengfei Zhou
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- P. R. China
| | - Xuping Wang
- School of Food Science and Engineering
- South China University of Technology
- Guangzhou 510640
- P. R. China
| | - Bo Yang
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- P. R. China
| | - Frank Hollmann
- Department of Biotechnology
- Delft University of Technology
- Delft
- The Netherlands
| | - Yonghua Wang
- School of Food Science and Engineering
- South China University of Technology
- Guangzhou 510640
- P. R. China
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15
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Scope, limitations and classification of lactamases. J Biotechnol 2016; 235:11-23. [DOI: 10.1016/j.jbiotec.2016.03.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
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16
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Devamani T, Rauwerdink AM, Lun-zer M, Jones BJ, Mooney JL, Tan MAO, Zhang ZJ, Xu JH, Dean AM, Kazlauskas RJ. Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases. J Am Chem Soc 2016; 138:1046-56. [PMID: 26736133 PMCID: PMC5466365 DOI: 10.1021/jacs.5b12209] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Catalytic promiscuity is a useful, but accidental, enzyme property, so finding catalytically promiscuous enzymes in nature is inefficient. Some ancestral enzymes were branch points in the evolution of new enzymes and are hypothesized to have been promiscuous. To test the hypothesis that ancestral enzymes were more promiscuous than their modern descendants, we reconstructed ancestral enzymes at four branch points in the divergence hydroxynitrile lyases (HNL's) from esterases ∼ 100 million years ago. Both enzyme types are α/β-hydrolase-fold enzymes and have the same catalytic triad, but differ in reaction type and mechanism. Esterases catalyze hydrolysis via an acyl enzyme intermediate, while lyases catalyze an elimination without an intermediate. Screening ancestral enzymes and their modern descendants with six esterase substrates and six lyase substrates found higher catalytic promiscuity among the ancestral enzymes (P < 0.01). Ancestral esterases were more likely to catalyze a lyase reaction than modern esterases, and the ancestral HNL was more likely to catalyze ester hydrolysis than modern HNL's. One ancestral enzyme (HNL1) along the path from esterase to hydroxynitrile lyases was especially promiscuous and catalyzed both hydrolysis and lyase reactions with many substrates. A broader screen tested mechanistically related reactions that were not selected for by evolution: decarboxylation, Michael addition, γ-lactam hydrolysis and 1,5-diketone hydrolysis. The ancestral enzymes were more promiscuous than their modern descendants (P = 0.04). Thus, these reconstructed ancestral enzymes are catalytically promiscuous, but HNL1 is especially so.
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Affiliation(s)
- Titu Devamani
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Alissa M. Rauwerdink
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Mark Lun-zer
- University of Minnesota, Department of Ecology, Evolution & Behavior and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Bryan J. Jones
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Joanna L. Mooney
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | | | - Zhi-Jun Zhang
- East China University of Science and Technology, School of Biotechnology, Meilong Road 130, Shanghai 200237 P. R. China
| | - Jian-He Xu
- East China University of Science and Technology, School of Biotechnology, Meilong Road 130, Shanghai 200237 P. R. China
| | - Antony M. Dean
- University of Minnesota, Department of Ecology, Evolution & Behavior and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
- Sun Yat-sen University, Institute of Ecology and Evolution, No.135, Xinggang West Road, Guangzhou, 510275 P. R. China
| | - Romas J. Kazlauskas
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
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17
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Efficient production of peracetic acid in aqueous solution with cephalosporin-deacetylating acetyl xylan esterase from Bacillus subtilis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Zago E, Durand E, Barouh N, Lecomte J, Villeneuve P, Aouf C. Synthesis of Lipophilic Antioxidants by a Lipase-B-Catalyzed Addition of Peracids to the Double Bond of 4-Vinyl-2-methoxyphenol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:9069-9075. [PMID: 26435061 DOI: 10.1021/acs.jafc.5b03551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
4-Vinyl guaiacol (2) was lipophilized through the electrophilic addition of peracids to its vinylic double bond. Those peracids were formed in situ, by the Candida antarctica lipase-B-assisted perhydrolysis of carboxylic acids ranging from C2 to C18, in hydrogen peroxide solution. The addition of peracids with 4-8 carbons in their alkyl chains led to the formation of two regioisomers, with the prevalence of hydroxyesters bearing a primary free hydroxyl (4c-4e). This prevalence became more pronounced when peracids with longer alkyl chains (C10-C18) were used. In this case, only isomers 4f-4h were formed. The antioxidant activity of the resulting hydroxyesters was assessed by means of the conjugated autoxidizable triene (CAT) assay, and it was found out that the 4-vinyl guaiacol antioxidant activity was significantly increased by grafting alkyl chains with 2-8 carbons.
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Affiliation(s)
- Erika Zago
- L'Unité Mixte de Recherche Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) , F-34060 Montpellier, France
| | - Erwann Durand
- L'Unité Mixte de Recherche Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) , F-34060 Montpellier, France
| | - Nathalie Barouh
- L'Unité Mixte de Recherche Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) , F-34060 Montpellier, France
| | - Jérôme Lecomte
- L'Unité Mixte de Recherche Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) , F-34060 Montpellier, France
| | - Pierre Villeneuve
- L'Unité Mixte de Recherche Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) , F-34060 Montpellier, France
| | - Chahinez Aouf
- L'Unité Mixte de Recherches (UMR) 1083 Sciences Pour l'Oenologie (SPO), Institut National de la Recherche Agronomique (INRA) , F-34060 Montpellier, France
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19
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China H, Okada Y, Ogino H. Production mechanism of active species on the oxidative bromination following perhydrolase activity. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hideyasu China
- Department of Applied Chemistry, College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Nakaku Sakai Osaka 599-8531 Japan
| | - Yutaka Okada
- Department of Applied Chemistry, College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Nakaku Sakai Osaka 599-8531 Japan
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20
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Sun Y, Zhao H, Wang J, Zhu J, Wu S. Identification and regulation of the catalytic promiscuity of (−)-γ-lactamase from Microbacterium hydrocarbonoxydans. Appl Microbiol Biotechnol 2015; 99:7559-68. [DOI: 10.1007/s00253-015-6503-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/17/2015] [Indexed: 02/02/2023]
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21
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Vojcic L, Pitzler C, Körfer G, Jakob F, Ronny Martinez, Maurer KH, Schwaneberg U. Advances in protease engineering for laundry detergents. N Biotechnol 2015; 32:629-34. [PMID: 25579194 DOI: 10.1016/j.nbt.2014.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/02/2014] [Accepted: 12/31/2014] [Indexed: 02/03/2023]
Abstract
Proteases are essential ingredients in modern laundry detergents. Over the past 30 years, subtilisin proteases employed in the laundry detergent industry have been engineered by directed evolution and rational design to tailor their properties towards industrial demands. This comprehensive review discusses recent success stories in subtilisin protease engineering. Advances in protease engineering for laundry detergents comprise simultaneous improvement of thermal resistance and activity at low temperatures, a rational strategy to modulate pH profiles, and a general hypothesis for how to increase promiscuous activity towards the production of peroxycarboxylic acids as mild bleaching agents. The three protease engineering campaigns presented provide in-depth analysis of protease properties and have identified principles that can be applied to improve or generate enzyme variants for industrial applications beyond laundry detergents.
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Affiliation(s)
- Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | | | | | - Felix Jakob
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany; EW-Nutrition GmbH, Enzyme Technology, Nattermannallee 1, D-50829 Köln, Germany
| | | | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, D-52074 Aachen, Germany.
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22
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Redirecting catalysis from proteolysis to perhydrolysis in subtilisin Carlsberg. J Biotechnol 2013; 167:279-86. [DOI: 10.1016/j.jbiotec.2013.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/17/2013] [Accepted: 06/27/2013] [Indexed: 11/23/2022]
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23
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Grover N, Dinu CZ, Kane RS, Dordick JS. Enzyme-based formulations for decontamination: current state and perspectives. Appl Microbiol Biotechnol 2013; 97:3293-300. [DOI: 10.1007/s00253-013-4797-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/15/2013] [Accepted: 02/18/2013] [Indexed: 11/28/2022]
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24
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Yin DT, Purpero VM, Fujii R, Jing Q, Kazlauskas RJ. New structural motif for carboxylic acid perhydrolases. Chemistry 2013; 19:3037-46. [PMID: 23325572 PMCID: PMC3784613 DOI: 10.1002/chem.201202027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 11/19/2012] [Indexed: 11/09/2022]
Abstract
Some serine hydrolases also catalyze a promiscuous reaction--reversible perhydrolysis of carboxylic acids to make peroxycarboxylic acids. Five X-ray crystal structures of these carboxylic acid perhydrolases show a proline in the oxyanion loop. Here, we test whether this proline is essential for high perhydrolysis activity using Pseudomonas fluorescens esterase (PFE). The L29P variant of this esterase catalyzes perhydrolysis 43-fold faster (k(cat) comparison) than the wild type. Surprisingly, saturation mutagenesis at the 29 position of PFE identified six other amino acid substitutions that increase perhydrolysis of acetic acid at least fourfold over the wild type. The best variant, L29I PFE, catalyzed perhydrolysis 83-times faster (k(cat) comparison) than wild-type PFE and twice as fast as L29P PFE. Despite the different amino acid in the oxyanion loop, L29I PFE shows a similar selectivity for hydrogen peroxide over water as L29P PFE (β(0)=170 vs. 160 M(-1)), and a similar fast formation of acetyl-enzyme (140 vs. 62 U mg(-1)). X-ray crystal structures of L29I PFE with and without bound acetate show an unusual mixture of two different oxyanion loop conformations. The type II β-turn conformation resembles the wild-type structure and is unlikely to increase perhydrolysis, but the type I β-turn conformation creates a binding site for a second acetate. Modeling suggests that a previously proposed mechanism for L29P PFE can be extended to include L29I PFE, so that an acetate accepts a hydrogen bond to promote faster formation of the acetyl-enzyme.
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Affiliation(s)
- DeLu Tyler Yin
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics, and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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25
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Kuban-Jankowska A, Tuszynski JA, Winter P, Gorska M, Knap N, Wozniak M. Activation of hydrogen peroxide to peroxytetradecanoic acid is responsible for potent inhibition of protein tyrosine phosphatase CD45. PLoS One 2012; 7:e52495. [PMID: 23300686 PMCID: PMC3531430 DOI: 10.1371/journal.pone.0052495] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 11/19/2012] [Indexed: 11/19/2022] Open
Abstract
Hydrogen peroxide induces oxidation and consequently inactivation of many protein tyrosine phosphatases. It was found that hydrogen peroxide, in the presence of carboxylic acids, was efficiently activated to form even more potent oxidant - peroxy acid. We have found that peroxytetradecanoic acid decreases the enzymatic activity of CD45 phosphatase significantly more than hydrogen peroxide. Our molecular docking computational analysis suggests that peroxytetradecanoic acid has a higher binding affinity to the catalytic center of CD45 than hydrogen peroxide.
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Affiliation(s)
- Alicja Kuban-Jankowska
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
- * E-mail: (AKJ); (MW)
| | - Jack A. Tuszynski
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Philip Winter
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Magdalena Gorska
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Narcyz Knap
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Michal Wozniak
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
- College of Health, Beauty Care and Education in Poznan, Faculty in Gdynia, Gdynia, Poland
- * E-mail: (AKJ); (MW)
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26
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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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27
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Yin DT, Kazlauskas RJ. Revised Molecular Basis of the Promiscuous Carboxylic Acid Perhydrolase Activity in Serine Hydrolases. Chemistry 2012; 18:8130-9. [DOI: 10.1002/chem.201200052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/09/2012] [Indexed: 11/08/2022]
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28
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Despotovic D, Vojcic L, Prodanovic R, Martinez R, Maurer KH, Schwaneberg U. Fluorescent Assay for Directed Evolution of Perhydrolases. ACTA ACUST UNITED AC 2012; 17:796-805. [DOI: 10.1177/1087057112438464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Directed evolution offers opportunities to improve promiscuous activities of hydrolases in rounds of diversity generation and high-throughput screening. In this article, we developed and validated a screening platform to improve the perhydrolytic activity of proteases and likely other hydrolases (e.g., lipases or esterases). Key was the development of a highly sensitive fluorescent assay (sensitivity in the µM range) based on 3-carboxy-7-hydroxycoumarin (HCC) formation. HCC is released through an hypobromite-mediated oxidation of 7-(4′-aminophenoxy)-3-carboxycoumarin (APCC), which enables for the first time a continuous measurement of peroxycarboxylic acid formation with a standard deviation of 11% in microtiter plates with a wide pH range window (5–9). As example, subtilisin Carlsberg was subjected to site saturation mutagenesis at position G165, yielding a variant T58A/G165L/L216W with 5.4-fold increased kcat for perhydrolytic activity compared with wild type.
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Affiliation(s)
| | | | - Radivoje Prodanovic
- RWTH Aachen University, Worringerweg, Aachen, Germany
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | | | - Karl-Heinz Maurer
- International Research Laundry & Home Care, Biotechnology, Düsseldorf, Germany
- Present address: AB Enzymes GmbH, Feldbergstraße, Darmstadt, Germany
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29
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Torres LL, Schließmann A, Schmidt M, Silva-Martin N, Hermoso JA, Berenguer J, Bornscheuer UT, Hidalgo A. Promiscuous enantioselective (−)-γ-lactamase activity in the Pseudomonas fluorescens esterase I. Org Biomol Chem 2012; 10:3388-92. [DOI: 10.1039/c2ob06887g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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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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31
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Jiang Y, Morley KL, Schrag JD, Kazlauskas RJ. Different active-site loop orientation in serine hydrolases versus acyltransferases. Chembiochem 2011; 12:768-76. [PMID: 21351219 DOI: 10.1002/cbic.201000693] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Indexed: 11/07/2022]
Abstract
Acyl transfer is a key reaction in biosynthesis, including synthesis of antibiotics and polyesters. Although researchers have long recognized the similar protein fold and catalytic machinery in acyltransferases and hydrolases, the molecular basis for the different reactivity has been a long-standing mystery. By comparison of X-ray structures, we identified a different oxyanion-loop orientation in the active site. In esterases/lipases a carbonyl oxygen points toward the active site, whereas in acyltransferases a NH of the main-chain amide points toward the active site. Amino acid sequence comparisons alone cannot identify such a difference in the main-chain orientation. To identify how this difference might change the reaction mechanism, we solved the X-ray crystal structure of Pseudomonas fluorescens esterase containing a sulfonate transition-state analogue bound to the active-site serine. This structure mimics the transition state for the attack of water on the acyl-enzyme and shows a bridging water molecule between the carbonyl oxygen mentioned above and the sulfonyl oxygen that mimics the attacking water. A possible mechanistic role for this bridging water molecule is to position and activate the attacking water molecule in hydrolases, but to deactivate the attacking water molecule in acyl transferases.
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Affiliation(s)
- Yun Jiang
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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32
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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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33
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Yin DLT, Bernhardt P, Morley KL, Jiang Y, Cheeseman JD, Purpero V, Schrag JD, Kazlauskas RJ. Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase. Biochemistry 2010; 49:1931-42. [PMID: 20112920 DOI: 10.1021/bi9021268] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many serine hydrolases catalyze perhydrolysis, the reversible formation of peracids from carboxylic acids and hydrogen peroxide. Recently, we showed that a single amino acid substitution in the alcohol binding pocket, L29P, in Pseudomonas fluorescens (SIK WI) aryl esterase (PFE) increased the specificity constant of PFE for peracetic acid formation >100-fold [Bernhardt et al. (2005) Angew. Chem., Int. Ed. 44, 2742]. In this paper, we extend this work to address the three following questions. First, what is the molecular basis of the increase in perhydrolysis activity? We previously proposed that the L29P substitution creates a hydrogen bond between the enzyme and hydrogen peroxide in the transition state. Here we report two X-ray structures of L29P PFE that support this proposal. Both structures show a main chain carbonyl oxygen closer to the active site serine as expected. One structure further shows acetate in the active site in an orientation consistent with reaction by an acyl-enzyme mechanism. We also detected an acyl-enzyme intermediate in the hydrolysis of epsilon-caprolactone by mass spectrometry. Second, can we further increase perhydrolysis activity? We discovered that the reverse reaction, hydrolysis of peracetic acid to acetic acid and hydrogen peroxide, occurs at nearly the diffusion limited rate. Since the reverse reaction cannot increase further, neither can the forward reaction. Consistent with this prediction, two variants with additional amino acid substitutions showed 2-fold higher k(cat), but K(m) also increased so the specificity constant, k(cat)/K(m), remained similar. Third, how does the L29P substitution change the esterase activity? Ester hydrolysis decreased for most esters (75-fold for ethyl acetate) but not for methyl esters. In contrast, L29P PFE catalyzed hydrolysis of epsilon-caprolactone five times more efficiently than wild-type PFE. Molecular modeling suggests that moving the carbonyl group closer to the active site blocks access for larger alcohol moieties but binds epsilon-caprolactone more tightly. These results are consistent with the natural function of perhydrolases being either hydrolysis of peroxycarboxylic acids or hydrolysis of lactones.
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Affiliation(s)
- De Lu Tyler Yin
- Department of Biochemistry, Molecular Biology, and Biophysics and The Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, USA
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Busto E, Gotor-Fernández V, Gotor V. Hydrolases: catalytically promiscuous enzymes for non-conventional reactions in organic synthesis. Chem Soc Rev 2010; 39:4504-23. [DOI: 10.1039/c003811c] [Citation(s) in RCA: 246] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0611-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Increased saccharification yields from aspen biomass upon treatment with enzymatically generated peracetic acid. Appl Biochem Biotechnol 2009; 160:1637-52. [PMID: 19484411 DOI: 10.1007/s12010-009-8639-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 04/05/2009] [Indexed: 10/20/2022]
Abstract
The recalcitrance of lignocellulosic biomass to enzymatic release of sugars (saccharification) currently limits its use as feedstock for biofuels. Enzymatic hydrolysis of untreated aspen wood releases only 21.8% of the available sugars due primarily to the lignin barrier. Nature uses oxidative enzymes to selectively degrade lignin in lignocellulosic biomass, but thus far, natural enzymes have been too slow for industrial use. In this study, oxidative pretreatment with commercial peracetic acid (470 mM) removed 40% of the lignin (from 19.9 to 12.0 wt.% lignin) from aspen and enhanced the sugar yields in subsequent enzymatic hydrolysis to about 90%. Increasing the amount of lignin removed correlated with increasing yields of sugar release. Unfortunately, peracetic acid is expensive, and concentrated forms can be hazardous. To reduce costs and hazards associated with using commercial peracetic acid, we used a hydrolase to catalyze the perhydrolysis of ethyl acetate generating 60-70 mM peracetic acid in situ as a pretreatment to remove lignin from aspen wood. A single pretreatment was insufficient, but multiple cycles (up to eight) removed up to 61.7% of the lignin enabling release of >90% of the sugars during saccharification. This value corresponds to a predicted 581 g of fermentable sugars from 1 kg of aspen wood. Improvements in the enzyme stability are needed before the enzymatically generated peracetic acid is a commercially viable alternative.
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37
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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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38
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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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39
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Hidalgo A, Schliessmann A, Molina R, Hermoso J, Bornscheuer UT. A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution. Protein Eng Des Sel 2008; 21:567-76. [PMID: 18559369 DOI: 10.1093/protein/gzn034] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein engineering is currently performed either by rational design, focusing in most cases on only a few positions modified by site-directed mutagenesis, or by directed molecular evolution, in which the entire protein-encoding gene is subjected to random mutagenesis followed by screening or selection of desired phenotypes. A novel alternative is focused directed evolution, in which only fragments of a protein are randomised while the overall scaffold of a protein remains unchanged. For this purpose, we developed a PCR technique using long, spiked oligonucleotides, which allow randomising of one or several cassettes in any given position of a gene. This method allows over 95% incorporation of mutations independently of their position within the gene, yielding sufficient product to generate large libraries, and the possibility of simultaneously randomising more than one locus at a time, thus originating recombination. The high efficiency of this method was verified by creating focused mutant libraries of Pseudomonas fluorescens esterase I (PFEI), screening for altered substrate selectivity and validating against libraries created by error-prone PCR. This led to the identification of two mutants within the OSCARR library with a 10-fold higher catalytic efficiency towards p-nitrophenyl dodecanoate. These PFEI variants were also modelled in order to explain the observed effects.
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Affiliation(s)
- Aurelio Hidalgo
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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40
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Bhattacharya S, Labutti JN, Seiner DR, Gates KS. Oxidative inactivation of protein tyrosine phosphatase 1B by organic hydroperoxides. Bioorg Med Chem Lett 2008; 18:5856-9. [PMID: 18595691 DOI: 10.1016/j.bmcl.2008.06.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 06/10/2008] [Accepted: 06/10/2008] [Indexed: 11/20/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are cysteine-dependent enzymes that play a central role in cell signaling. Organic hydroperoxides cause thiol-reversible, oxidative inactivation of PTP1B in a manner that mirrors the endogenous signaling agent hydrogen peroxide.
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Affiliation(s)
- Sanjib Bhattacharya
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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41
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Piret G, Coffinier Y, Roux C, Melnyk O, Boukherroub R. Biomolecule and nanoparticle transfer on patterned and heterogeneously wetted superhydrophobic silicon nanowire surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:1670-1672. [PMID: 18251564 DOI: 10.1021/la703985w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report on the use of patterned superhydrophobic silicon nanowire surfaces for the efficient, selective transfer of biological molecules and nanoparticles. Superhydrophilic patterns are prepared on superhydrophobic silicon nanowire surfaces using standard optical lithography. The resulting water-repellent surface allows material transfer and physisorption to the superhydrophilic islands upon exposure to an aqueous solution containing peptides, proteins, or nanoparticles.
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Affiliation(s)
- Gaëlle Piret
- Institut de Recherche Interdisciplinaire CNRS-USR 3078 Cité Scientifique, Avenue Poincaré - B.P. 60069, 59652 Villeneuve d'Ascq, France
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42
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Li C, Hassler M, Bugg TDH. Catalytic Promiscuity in the α/β-Hydrolase Superfamily: Hydroxamic Acid Formation, CC Bond Formation, Ester and Thioester Hydrolysis in the CC Hydrolase Family. Chembiochem 2008; 9:71-6. [DOI: 10.1002/cbic.200700428] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Qian Z, Fields CJ, Yu Y, Lutz S. Recent progress in engineering alpha/beta hydrolase-fold family members. Biotechnol J 2007; 2:192-200. [PMID: 17183507 DOI: 10.1002/biot.200600186] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The members of the alpha/beta hydrolase-fold family represent a functionally versatile group of enzymes with many important applications in biocatalysis. Given the technical significance of alpha/beta hydrolases in processes ranging from the kinetic resolution of enantiomeric precursors for pharmaceutical compounds to bulk products such as laundry detergent, optimizing and tailoring enzymes for these applications presents an ongoing challenge to chemists, biochemists, and engineers alike. A review of the recent literature on alpha/beta hydrolase engineering suggests that the early successes of "random processes" such as directed evolution are now being slowly replaced by more hypothesis-driven, focused library approaches. These developments reflect a better understanding of the enzymes' structure-function relationship and improved computational resources, which allow for more sophisticated search and prediction algorithms, as well as, in a very practical sense, the realization that bigger is not always better.
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Affiliation(s)
- Zhen Qian
- Emory University, Department of Chemistry, Atlanta, GA, USA
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44
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Vaillancourt FH, Yeh E, Vosburg DA, Garneau-Tsodikova S, Walsh CT. Nature's inventory of halogenation catalysts: oxidative strategies predominate. Chem Rev 2007; 106:3364-78. [PMID: 16895332 DOI: 10.1021/cr050313i] [Citation(s) in RCA: 408] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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45
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Toscano MD, Woycechowsky KJ, Hilvert D. Minimalist active-site redesign: teaching old enzymes new tricks. Angew Chem Int Ed Engl 2007; 46:3212-36. [PMID: 17450624 DOI: 10.1002/anie.200604205] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although nature evolves its catalysts over millions of years, enzyme engineers try to do it a bit faster. Enzyme active sites provide highly optimized microenvironments for the catalysis of biologically useful chemical transformations. Consequently, changes at these centers can have large effects on enzyme activity. The prediction and control of these effects provides a promising way to access new functions. The development of methods and strategies to explore the untapped catalytic potential of natural enzyme scaffolds has been pushed by the increasing demand for industrial biocatalysts. This Review describes the use of minimal modifications at enzyme active sites to expand their catalytic repertoires, including targeted mutagenesis and the addition of new reactive functionalities. Often, a novel activity can be obtained with only a single point mutation. The many successful examples of active-site engineering through minimal mutations give useful insights into enzyme evolution and open new avenues in biocatalyst research.
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Affiliation(s)
- Miguel D Toscano
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, Switzerland
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46
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Toscano M, Woycechowsky K, Hilvert D. Minimale Umgestaltung aktiver Enzymtaschen – wie man alten Enzymen neue Kunststücke beibringt. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604205] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Kataoka M, Honda K, Sakamoto K, Shimizu S. Microbial enzymes involved in lactone compound metabolism and their biotechnological applications. Appl Microbiol Biotechnol 2007; 75:257-66. [PMID: 17333168 DOI: 10.1007/s00253-007-0896-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 02/15/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
Lactone compounds are widely distributed in nature and play important roles in organisms. These compounds are synthesized and metabolized enzymatically in vivo; however, detailed investigation of these enzymes lags behind that of other common enzymes. In this paper, recent work on the enzymes involved in the metabolism of lactone compounds will be reviewed. In particular, fundamental and application studies on lactonases and Baeyer-Villiger monooxgenases of microbial origin are described.
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Affiliation(s)
- Michihiko Kataoka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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48
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Li JJ, Bugg TDH. Investigation of a general base mechanism for esterhydrolysis in C–C hydrolase enzymes of the α/β-hydrolase superfamily: a novel mechanism for the serine catalytic triad. Org Biomol Chem 2007; 5:507-13. [PMID: 17252134 DOI: 10.1039/b615605c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Previous mechanistic and crystallographic studies on two C-C hydrolase enzymes, Escherichia coli MhpC and Burkholderia xenovorans BphD, support a general base mechanism for C-C hydrolytic cleavage, rather than the nucleophilic mechanism expected for a serine hydrolase. The role of the active site serine residue could be to form a hydrogen bond with a gem-diolate intermediate, or to protonate such an intermediate. Hydrolase BphD is able to catalyse the hydrolysis of p-nitrophenyl benzoate ester substrates, which has enabled an investigation of these mechanisms using a Hammett analysis, and comparative studies upon five serine esterases and lipases from the alpha/beta-hydrolase family. A reaction parameter (rho) value of +0.98 was measured for BphD-catalysed ester hydrolysis, implying a build-up of negative charge in the transition state, consistent with a general base mechanism. Values of +0.31-0.61 were measured for other serine esterases and lipases, for the same series of esterase substrates. Pre-steady state kinetic studies of ester hydrolysis, using p-nitrophenyl acetate as the substrate, revealed a single step kinetic mechanism for BphD-catalysed ester hydrolysis, with no burst kinetics. A general base mechanism for BphD-catalysed ester hydrolysis is proposed, in which Ser-112 stabilises an oxyanion intermediate through hydrogen bonding, and assists the rotation of this oxyanion intermediate via proton transfer, a novel reaction mechanism for the serine catalytic triad.
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Affiliation(s)
- Jian-Jun Li
- Department of Chemistry, University of Warwick, Coventry, UK CV4 7AL
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49
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Carboni-Oerlemans C, Domínguez de María P, Tuin B, Bargeman G, van der Meer A, van Gemert R. Hydrolase-catalysed synthesis of peroxycarboxylic acids: Biocatalytic promiscuity for practical applications. J Biotechnol 2006; 126:140-51. [PMID: 16730828 DOI: 10.1016/j.jbiotec.2006.04.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 03/31/2006] [Accepted: 04/07/2006] [Indexed: 11/18/2022]
Abstract
The enzymatic promiscuity concept involves the possibility that one active site of an enzyme can catalyse several different chemical transformations. A rational understanding of the mechanistic reasons for this catalytic performance could lead to new practical applications. The capability of certain hydrolases to perform the perhydrolysis was described more than a decade ago, and recently its molecular basis has been elucidated. Remarkably, a similarity between perhydrolases (cofactor-free haloperoxidases) and serine hydrolases was found, with both groups of enzymes sharing a common catalytic triad, which suggests an evolution from a common ancestor. On the other hand, several biotechnological applications derived from the capability of hydrolases to catalyse the synthesis of peracids have been reported: the use of hydrolases as bleaching agents via in situ generation of peracids; (self)-epoxidation of unsaturated fatty acids, olefins, or plant oils, via Prileshajev epoxidation; Baeyer-Villiger reactions. In the present review, the molecular basis for this promiscuous hydrolase capability, as well as identified applications are reviewed and described in detail.
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Affiliation(s)
- Chiara Carboni-Oerlemans
- Akzo Nobel Chemicals BV, Chemicals Process Technology Department (CPT), Velperweg 76, PO Box 9300, 6800 SB Arnhem, The Netherlands.
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50
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Braiuca P, Ebert C, Basso A, Linda P, Gardossi L. Computational methods to rationalize experimental strategies in biocatalysis. Trends Biotechnol 2006; 24:419-25. [PMID: 16870286 DOI: 10.1016/j.tibtech.2006.07.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 05/24/2006] [Accepted: 07/12/2006] [Indexed: 11/15/2022]
Abstract
Computational methods are more and more widely applied in biocatalysis to gain rational guidelines, to orient experimental planning and, ultimately, to avoid expensive and time-consuming experiments. In this respect, molecular modelling, multivariate statistical analysis and chemometrics in general are useful computational tools, although they follow completely different investigative approaches.
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Affiliation(s)
- Paolo Braiuca
- Laboratory of Applied and Computational Biocatalysis, Dipartimento di Scienze Farmaceutiche, Università degli Studi, Piazzale Europa 1, 34127 Trieste, Italy
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