1
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Li X, Li C, Qu G, Yuan B, Sun Z. Engineering of a Baeyer-Villiger monooxygenase to Improve Substrate Scope, Stereoselectivity and Regioselectivity. Chembiochem 2024; 25:e202400328. [PMID: 38742991 DOI: 10.1002/cbic.202400328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Baeyer-Villiger monooxygenases belong to a family of flavin-binding proteins that catalyze the Baeyer-Villiger (BV) oxidation of ketones to produce lactones or esters, which are important intermediates in pharmaceuticals or sustainable materials. Phenylacetone monooxygenase (PAMO) from Thermobifida fusca with moderate thermostability catalyzes the oxidation of aryl ketone substrates, but is limited by high specificity and narrow substrate scope. In the present study, we applied loop optimization by loop swapping followed by focused saturation mutagenesis in order to evolve PAMO mutants capable of catalyzing the regioselective BV oxidation of cyclohexanone and cyclobutanone derivatives with formation of either normal or abnormal esters or lactones. We further modulated PAMO to increase enantioselectivity. Crystal structure studies indicate that rotation occurs in the NADP-binding domain and that the high B-factor region is predominantly distributed in the catalytic pocket residues. Computational analyses further revealed dynamic character in the catalytic pocket and reshaped hydrogen bond interaction networks, which is more favorable for substrate binding. Our study provides useful insights for studying enzyme-substrate adaptations.
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Affiliation(s)
- Xu Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
| | - Congcong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
| | - Bo Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China
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2
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Chen X, Zhang X, Qin M, Chen J, Wang M, Liu Z, An L, Song X, Yao L. Protein Allostery Study in Cells Using NMR Spectroscopy. Anal Chem 2024; 96:7065-7072. [PMID: 38652079 DOI: 10.1021/acs.analchem.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Protein allostery is commonly observed in vitro. But how protein allostery behaves in cells is unknown. In this work, a protein monomer-dimer equilibrium system was built with the allosteric effect on the binding characterized using NMR spectroscopy through mutations away from the dimer interface. A chemical shift linear fitting method was developed that enabled us to accurately determine the dissociation constant. A total of 28 allosteric mutations were prepared and grouped to negative allosteric, nonallosteric, and positive allosteric modulators. ∼ 50% of mutations displayed the allosteric-state changes when moving from a buffered solution into cells. For example, there were no positive allosteric modulators in the buffered solution but eight in cells. The change in protein allostery is correlated with the interactions between the protein and the cellular environment. These interactions presumably drive the surrounding macromolecules in cells to transiently bind to the monomer and dimer mutational sites and change the free energies of the two species differently which generate new allosteric effects. These surrounding macromolecules create a new protein allostery pathway that is only present in cells.
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Affiliation(s)
- Xiaoxu Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xueying Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Qin
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Jingfei Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Mengting Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Liaoyuan An
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiangfei Song
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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3
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Engineering Rieske oxygenase activity one piece at a time. Curr Opin Chem Biol 2023; 72:102227. [PMID: 36410250 PMCID: PMC9939785 DOI: 10.1016/j.cbpa.2022.102227] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022]
Abstract
Enzyme engineering plays a central role in the development of biocatalysts for biotechnology, chemical and pharmaceutical manufacturing, and environmental remediation. Rational design of proteins has historically relied on targeting active site residues to confer a protein with desirable catalytic properties. However, additional "hotspots" are also known to exist beyond the active site. Structural elements such as subunit-subunit interactions, entrance tunnels, and flexible loops influence enzyme catalysis and serve as potential "hotspots" for engineering. For the Rieske oxygenases, which use a Rieske cluster and mononuclear iron center to catalyze a challenging set of reactions, these outside of the active site regions are increasingly being shown to drive catalytic outcomes. Therefore, here, we highlight recent work on structurally characterized Rieske oxygenases that implicates architectural pieces inside and outside of the active site as key dictators of catalysis, and we suggest that these features may warrant attention in efforts aimed at Rieske oxygenase engineering.
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4
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Núñez-Navarro N, Salazar Muñoz J, Castillo F, Ramírez-Sarmiento CA, Poblete-Castro I, Zacconi FC, Parra LP. Discovery of New Phenylacetone Monooxygenase Variants for the Development of Substituted Indigoids through Biocatalysis. Int J Mol Sci 2022; 23:ijms232012544. [PMID: 36293414 PMCID: PMC9604523 DOI: 10.3390/ijms232012544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Indigoids are natural pigments obtained from plants by ancient cultures. Romans used them mainly as dyes, whereas Asian cultures applied these compounds as treatment agents for several diseases. In the modern era, the chemical industry has made it possible to identify and develop synthetic routes to obtain them from petroleum derivatives. However, these processes require high temperatures and pressures and large amounts of solvents, acids, and alkali agents. Thus, enzyme engineering and the development of bacteria as whole-cell biocatalysts emerges as a promising green alternative to avoid the use of these hazardous materials and consequently prevent toxic waste generation. In this research, we obtained two novel variants of phenylacetone monooxygenase (PAMO) by iterative saturation mutagenesis. Heterologous expression of these two enzymes, called PAMOHPCD and PAMOHPED, in E. coli was serendipitously found to produce indigoids. These interesting results encourage us to characterize the thermal stability and enzyme kinetics of these new variants and to evaluate indigo and indirubin production in a whole-cell system by HPLC. The highest yields were obtained with PAMOHPCD supplemented with L-tryptophan, producing ~3000 mg/L indigo and ~130.0 mg/L indirubin. Additionally, both enzymes could oxidize and produce several indigo derivatives from substituted indoles, with PAMOHPCD being able to produce the well-known Tyrian purple. Our results indicate that the PAMO variants described herein have potential application in the textile, pharmaceutics, and semiconductors industries, prompting the use of environmentally friendly strategies to obtain a diverse variety of indigoids.
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Affiliation(s)
- Nicolás Núñez-Navarro
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Javier Salazar Muñoz
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
| | - Francisco Castillo
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Department of Chemical and Bioprocess Engineering, Universidad de Santiago de Chile (USACH), Santiago 8350709, Chile
| | - Flavia C. Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
- Correspondence: (F.C.Z.); (L.P.P.)
| | - Loreto P. Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Correspondence: (F.C.Z.); (L.P.P.)
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5
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Focused mutagenesis in non-catalytic cavity for improving catalytic efficiency of 3-ketosteroid-Δ1-dehydrogenase. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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“Nonpolarity paving” in substrate tunnel of a Limnobacter sp. Phenylacetone monooxygenase for efficient single whole-cell synthesis of esomeprazole. Bioorg Chem 2022; 125:105867. [DOI: 10.1016/j.bioorg.2022.105867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
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7
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Ding Y, Perez-Ortiz G, Peate J, Barry SM. Redesigning Enzymes for Biocatalysis: Exploiting Structural Understanding for Improved Selectivity. Front Mol Biosci 2022; 9:908285. [PMID: 35936784 PMCID: PMC9355150 DOI: 10.3389/fmolb.2022.908285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
The discovery of new enzymes, alongside the push to make chemical processes more sustainable, has resulted in increased industrial interest in the use of biocatalytic processes to produce high-value and chiral precursor chemicals. Huge strides in protein engineering methodology and in silico tools have facilitated significant progress in the discovery and production of enzymes for biocatalytic processes. However, there are significant gaps in our knowledge of the relationship between enzyme structure and function. This has demonstrated the need for improved computational methods to model mechanisms and understand structure dynamics. Here, we explore efforts to rationally modify enzymes toward changing aspects of their catalyzed chemistry. We highlight examples of enzymes where links between enzyme function and structure have been made, thus enabling rational changes to the enzyme structure to give predictable chemical outcomes. We look at future directions the field could take and the technologies that will enable it.
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8
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Karamitros CS, Murray K, Winemiller B, Lamb C, Stone EM, D'Arcy S, Johnson KA, Georgiou G. Leveraging intrinsic flexibility to engineer enhanced enzyme catalytic activity. Proc Natl Acad Sci U S A 2022; 119:e2118979119. [PMID: 35658075 PMCID: PMC9191678 DOI: 10.1073/pnas.2118979119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Dynamic motions of enzymes occurring on a broad range of timescales play a pivotal role in all steps of the reaction pathway, including substrate binding, catalysis, and product release. However, it is unknown whether structural information related to conformational flexibility can be exploited for the directed evolution of enzymes with higher catalytic activity. Here, we show that mutagenesis of residues exclusively located at flexible regions distal to the active site of Homo sapiens kynureninase (HsKYNase) resulted in the isolation of a variant (BF-HsKYNase) in which the rate of the chemical step toward kynurenine was increased by 45-fold. Mechanistic pre–steady-state kinetic analysis of the wild type and the evolved enzyme shed light on the underlying effects of distal mutations (>10 Å from the active site) on the rate-limiting step of the catalytic cycle. Hydrogen-deuterium exchange coupled to mass spectrometry and molecular dynamics simulations revealed that the amino acid substitutions in BF-HsKYNase allosterically affect the flexibility of the pyridoxal-5′-phosphate (PLP) binding pocket, thereby impacting the rate of chemistry, presumably by altering the conformational ensemble and sampling states more favorable to the catalyzed reaction.
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Affiliation(s)
| | - Kyle Murray
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080
| | - Brent Winemiller
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Everett M. Stone
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX 78712
- LiveSTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78712
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080
| | - Kenneth A. Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX 78712
- LiveSTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78712
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
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9
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Qu G, Bi Y, Liu B, Li J, Han X, Liu W, Jiang Y, Qin Z, Sun Z. Unlocking the Stereoselectivity and Substrate Acceptance of Enzymes: Proline‐Induced Loop Engineering Test. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
| | - Yuexin Bi
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- University of Science and Technology of China Hefei 230027 China
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
| | - Junkuan Li
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- Department of Chemistry School of Science Tianjin University Tianjin 300072 China
| | - Xu Han
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
| | - Yingying Jiang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zongmin Qin
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
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10
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Qu G, Bi Y, Liu B, Li J, Han X, Liu W, Jiang Y, Qin Z, Sun Z. Unlocking the Stereoselectivity and Substrate Acceptance of Enzymes: Proline-Induced Loop Engineering Test. Angew Chem Int Ed Engl 2021; 61:e202110793. [PMID: 34658118 DOI: 10.1002/anie.202110793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Indexed: 12/12/2022]
Abstract
Protein stability and evolvability influence each other. Although protein dynamics play essential roles in various catalytically important properties, their high flexibility and diversity makes it difficult to incorporate such properties into rational engineering. Therefore, how to unlock the potential evolvability in a user-friendly rational design process remains a challenge. In this endeavor, we describe a method for engineering an enantioselective alcohol dehydrogenase. It enables synthetically important substrate acceptance for 4-chlorophenyl pyridine-2-yl ketone, and perfect stereocontrol of both (S)- and (R)-configured products. Thermodynamic analysis unveiled the subtle interaction between enzyme stability and evolvability, while computational studies provided insights into the origin of selectivity and substrate recognition. Preparative-scale synthesis of the (S)-product (73 % yield; >99 % ee) was performed on a gram-scale. This proof-of-principle study demonstrates that interfaced proline residues can be rationally engineered to unlock evolvability and thus provide access to new biocatalysts with highly improved catalytic performance.
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Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yuexin Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Science and Technology of China, Hefei, 230027, China
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Junkuan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Department of Chemistry, School of Science, Tianjin University, Tianjin, 300072, China
| | - Xu Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yingying Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongmin Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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11
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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12
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Harwood LA, Wong LL, Robertson J. Enzymatic Kinetic Resolution by Addition of Oxygen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lucy A. Harwood
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Luet L. Wong
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
| | - Jeremy Robertson
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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13
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Harwood LA, Wong LL, Robertson J. Enzymatic Kinetic Resolution by Addition of Oxygen. Angew Chem Int Ed Engl 2021; 60:4434-4447. [PMID: 33037837 PMCID: PMC7986699 DOI: 10.1002/anie.202011468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 12/25/2022]
Abstract
Kinetic resolution using biocatalysis has proven to be an excellent complementary technique to traditional asymmetric catalysis for the production of enantioenriched compounds. Resolution using oxidative enzymes produces valuable oxygenated structures for use in synthetic route development. This Minireview focuses on enzymes which catalyse the insertion of an oxygen atom into the substrate and, in so doing, can achieve oxidative kinetic resolution. The Baeyer-Villiger rearrangement, epoxidation, and hydroxylation are included, and biological advancements in enzyme development, and applications of these key enantioenriched intermediates in natural product synthesis are discussed.
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Affiliation(s)
- Lucy A. Harwood
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RoadOxfordOX1 3QRUK
- Oxford Suzhou Centre for Advanced ResearchRuo Shui Road, Suzhou Industrial ParkJiangsu215123P. R. China
| | - Jeremy Robertson
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Oxford Suzhou Centre for Advanced ResearchRuo Shui Road, Suzhou Industrial ParkJiangsu215123P. R. China
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14
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Yu J, Yang J, Seok C, Song WJ. Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes. Chem Sci 2021; 12:5091-5101. [PMID: 34168770 PMCID: PMC8179601 DOI: 10.1039/d0sc06823c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Directed evolution has provided us with great opportunities and prospects in the synthesis of tailor-made proteins. It, however, often requires at least mid to high throughput screening, necessitating more effective strategies for laboratory evolution. We herein demonstrate that protein symmetry can be a versatile criterion for searching for promising hotspots for the directed evolution of de novo oligomeric enzymes. The randomization of symmetry-related residues located at the rotational axes of artificial metallo-β-lactamase yields drastic effects on catalytic activities, whereas that of non-symmetry-related, yet, proximal residues to the active site results in negligible perturbations. Structural and biochemical analysis of the positive hits indicates that seemingly trivial mutations at symmetry-related spots yield significant alterations in overall structures, metal-coordination geometry, and chemical environments of active sites. Our work implicates that numerous artificially designed and natural oligomeric proteins might have evolutionary advantages of propagating beneficial mutations using their global symmetry. Symmetry-related residues located at the rotational axes can be promising hotspots for the evolution of de novo oligomeric enzymes even though they are distantly located from the active site pocket.![]()
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Affiliation(s)
- Jaeseung Yu
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Jinsol Yang
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Chaok Seok
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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15
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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16
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Ren SM, Liu F, Wu YQ, Chen Q, Zhang ZJ, Yu HL, Xu JH. Identification two key residues at the intersection of domains of a thioether monooxygenase for improving its sulfoxidation performance. Biotechnol Bioeng 2020; 118:737-744. [PMID: 33073356 DOI: 10.1002/bit.27604] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/20/2020] [Accepted: 10/11/2020] [Indexed: 02/01/2023]
Abstract
AcCHMO, a cyclohexanone monooxygenase from Acinetobacter calcoaceticus, is a typical Type I Baeyer-Villiger monooxygenase (BVMO). We previously obtained the AcCHMOM6 mutant, which oxidizes omeprazole sulfide (OPS) to the chiral sulfoxide drug esomeprazole. To further improve the catalytic efficiency of the AcCHMOM6 mutant, a focused mutagenesis strategy was adopted at the intersections of the FAD-binding domain, NADPH-binding domain, and α-helical domain based on structural characteristics of AcCHMO. By using focused mutagenesis and subsequent global evolution two key residues (L55 and P497) at the intersections of the domains were identified. Mutant of L55Y improved catalytic efficiency significantly, whereas the P497S mutant alleviated substrate inhibition remarkably. AcCHMOM7 (L55Y/P497S) was obtained by combining the two mutations, which increased the specific activity from 18.5 (M6) to 108 U/g, and an increase in the Ki of the substrate OPS from 34 to 265 μM. The results indicate that catalytic performance can be elevated by modification of the sensitive sites at the intersection of the domains of AcCHMO. The results also provided some insights for the engineering of other Type I BVMOs or other multidomain proteins.
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Affiliation(s)
- Shi-Miao Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yin-Qi Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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17
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Hu Y, Xu W, Hui C, Xu J, Huang M, Lin X, Wu Q. The mutagenesis of a single site for enhancing or reversing the enantio- or regiopreference of cyclohexanone monooxygenases. Chem Commun (Camb) 2020; 56:9356-9359. [PMID: 32672300 DOI: 10.1039/d0cc03721d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mutagenesis of a "second sphere" switch residue of CHMOAcineto could control its enantio- and regiopreference. Replacing phenylalanine (F) at position 277 of CHMOAcineto into larger tryptophan (W) enabled a significant enhancement of enantio- or regioselectivity toward structurally diverse substrates, moreover, a complete reversal of enantio- or regiopreference was realized by mutating F277 into a range of smaller amino acids (A/C/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/V).
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Affiliation(s)
- Yujing Hu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China.
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18
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201901491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Deutschland
- Department of Chemistry, Hans-Meerwein-Straße 4 Philipps-Universität 35032 Marburg Deutschland
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19
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. Angew Chem Int Ed Engl 2020; 59:13204-13231. [PMID: 31267627 DOI: 10.1002/anie.201901491] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Department of Chemistry, Hans-Meerwein-Strasse 4 Philipps-University 35032 Marburg Germany
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20
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Natural Variation in the ‘Control Loop’ of BVMOAFL210 and Its Influence on Regioselectivity and Sulfoxidation. Catalysts 2020. [DOI: 10.3390/catal10030339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are flavin-dependent enzymes that primarily convert ketones to esters, but can also catalyze heteroatom oxidation. Several structural studies have highlighted the importance of the ‘control loop’ in BVMOs, which adopts different conformations during catalysis. Central to the ‘control loop’ is a conserved tryptophan that has been implicated in NADP(H) binding. BVMOAFL210 from Aspergillus flavus, however, contains a threonine in the equivalent position. Here, we report the structure of BVMOAFL210 in complex with NADP+ in both the ‘open’ and ‘closed’ conformations. In neither conformation does Thr513 contact the NADP+. Although mutagenesis of Thr513 did not significantly alter the substrate scope, changes in peroxyflavin stability and reaction rates were observed. Mutation of this position also brought about changes in the regio- and enantioselectivity of the enzyme. Moreover, lower rates of overoxidation during sulfoxidation of thioanisole were also observed.
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21
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Unbiased libraries in protein directed evolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140321. [DOI: 10.1016/j.bbapap.2019.140321] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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22
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Schmidt S, Bornscheuer UT. Baeyer-Villiger monooxygenases: From protein engineering to biocatalytic applications. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:231-281. [DOI: 10.1016/bs.enz.2020.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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23
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Fürst MJLJ, Fiorentini F, Fraaije MW. Beyond active site residues: overall structural dynamics control catalysis in flavin-containing and heme-containing monooxygenases. Curr Opin Struct Biol 2019; 59:29-37. [DOI: 10.1016/j.sbi.2019.01.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
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24
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Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites. Sci Rep 2019; 9:16957. [PMID: 31740686 PMCID: PMC6861286 DOI: 10.1038/s41598-019-53464-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/24/2019] [Indexed: 11/27/2022] Open
Abstract
For protein mutagenesis, a common expectation is that important positions will behave like on/off “toggle” switches (i.e., a few substitutions act like wildtype, most abolish function). However, there exists another class of important positions that manifests a wide range of functional outcomes upon substitution: “rheostat” positions. Previously, we evaluated rheostat positions located near the allosteric binding sites for inhibitor alanine (Ala) and activator fructose-1,6-bisphosphate (Fru-1,6-BP) in human liver pyruvate kinase. When substituted with multiple amino acids, many positions demonstrated moderate rheostatic effects on allosteric coupling between effector binding and phosphoenolpyruvate (PEP) binding in the active site. Nonetheless, the combined outcomes of all positions sampled the full range of possible allosteric coupling (full tunability). However, that study only evaluated allosteric tunability of “local” positions, i.e., positions were located near the binding sites of the allosteric ligand being assessed. Here, we evaluated tunability of allosteric coupling when mutated sites were distant from the allosterically-coupled binding sites. Positions near the Ala binding site had rheostatic outcomes on allosteric coupling between Fru-1,6-BP and PEP binding. In contrast, positions in the Fru-1,6-BP site exhibited modest effects on coupling between Ala and PEP binding. Analyzed in aggregate, both PEP/Ala and PEP/Fru-1,6-BP coupling were again fully tunable by amino acid substitutions at this limited set of distant positions. Furthermore, some positions exhibited rheostatic control over multiple parameters and others exhibited rheostatic effects on one parameter and toggle control over a second. These findings highlight challenges in efforts to both predict/interpret mutational outcomes and engineer functions into proteins.
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25
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Fürst MJLJ, Gran-Scheuch A, Aalbers FS, Fraaije MW. Baeyer–Villiger Monooxygenases: Tunable Oxidative Biocatalysts. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03396] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maximilian J. L. J. Fürst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Alejandro Gran-Scheuch
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Friso S. Aalbers
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
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26
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Fürst MJLJ, Romero E, Gómez Castellanos JR, Fraaije MW, Mattevi A. Side-Chain Pruning Has Limited Impact on Substrate Preference in a Promiscuous Enzyme. ACS Catal 2018; 8:11648-11656. [PMID: 30687578 PMCID: PMC6345240 DOI: 10.1021/acscatal.8b03793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/26/2018] [Indexed: 01/02/2023]
Abstract
![]()
Detoxifying
enzymes such as flavin-containing monooxygenases deal
with a huge array of highly diverse xenobiotics and toxic compounds.
In addition to being of high physiological relevance, these drug-metabolizing
enzymes are useful catalysts for synthetic chemistry. Despite the
wealth of studies, the molecular basis of their relaxed substrate
selectivity remains an open question. Here, we addressed this issue
by applying a cumulative alanine mutagenesis approach to cyclohexanone
monooxygenase from Thermocrispum municipale, a flavin-dependent
Baeyer–Villiger monooxygenase which we chose as a model system
because of its pronounced thermostability and substrate promiscuity.
Simultaneous removal of up to eight noncatalytic active-site side
chains including four phenylalanines had no effect on protein folding,
thermostability, and cofactor loading. We observed a linear decrease
in activity, rather than a selectivity switch, and attributed this
to a less efficient catalytic environment in the enlarged active-site
space. Time-resolved kinetic studies confirmed this interpretation.
We also determined the crystal structure of the enzyme in complex
with a mimic of the reaction intermediate that shows an unaltered
overall protein conformation. These findings led us to propose that
this cyclohexanone monooxygenase may lack a distinct substrate selection
mechanism altogether. We speculate that the main or exclusive function
of the protein shell in promiscuous enzymes might be the stabilization
and accessibility of their very reactive catalytic intermediates.
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Affiliation(s)
- Maximilian J. L. J. Fürst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | | | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
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27
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Alternative Splicing of the Aflatoxin-Associated Baeyer⁻Villiger Monooxygenase from Aspergillus flavus: Characterisation of MoxY Isoforms. Toxins (Basel) 2018; 10:toxins10120521. [PMID: 30563144 PMCID: PMC6315744 DOI: 10.3390/toxins10120521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/01/2018] [Accepted: 12/03/2018] [Indexed: 01/24/2023] Open
Abstract
Aflatoxins are carcinogenic mycotoxins that are produced by the filamentous fungus Aspergillus flavus, a contaminant of numerous food crops. Aflatoxins are synthesised via the aflatoxin biosynthesis pathway, with the enzymes involved encoded by the aflatoxin biosynthesis gene cluster. MoxY is a type I Baeyer–Villiger monooxygenase (BVMO), responsible for the conversion of hydroxyversicolorone (HVN) and versicolorone (VN) to versiconal hemiacetal acetate (VHA) and versiconol acetate (VOAc), respectively. Using mRNA data, an intron near the C-terminus was identified that is alternatively spliced, creating two possible MoxY isoforms which exist in vivo, while analysis of the genomic DNA suggests an alternative start codon leading to possible elongation of the N-terminus. These four variants of the moxY gene were recombinantly expressed in Escherichia coli, and their activity evaluated with respect to their natural substrates HVN and VN, as well as surrogate ketone substrates. Activity of the enzyme is absolutely dependent on the additional 22 amino acid residues at the N-terminus. Two MoxY isoforms with alternative C-termini, MoxYAltN and MoxYAltNC, converted HVN and VN, in addition to a range of ketone substrates. Stability and flavin-binding data suggest that MoxYAltN is, most likely, the dominant isoform. MoxYAltNC is generated by intron splicing, in contrast to intron retention, which is the most prevalent type of alternative splicing in ascomycetes. The alternative C-termini did not alter the substrate acceptance profile, or regio- or enantioselectivity of the enzyme, but did significantly affect the solubility and stability.
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28
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Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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29
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Li A, Sun Z, Reetz MT. Solid-Phase Gene Synthesis for Mutant Library Construction: The Future of Directed Evolution? Chembiochem 2018; 19:2023-2032. [PMID: 30044530 DOI: 10.1002/cbic.201800339] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of, Bio-resources; Hubei Key Laboratory of Industrial Biotechnology; College of Life Sciences; Hubei University; 368 Youyi Road Wuchang Wuhan 430062 China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
- Department of Chemistry; Philipps University; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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30
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Buller AR, van Roye P, Cahn JK, Scheele RA, Herger M, Arnold FH. Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble. J Am Chem Soc 2018; 140:7256-7266. [PMID: 29712420 PMCID: PMC5999571 DOI: 10.1021/jacs.8b03490] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric enzymes contain a wealth of catalytic diversity that remains distinctly underutilized for biocatalysis. Tryptophan synthase is a model allosteric system and a valuable enzyme for the synthesis of noncanonical amino acids (ncAA). Previously, we evolved the β-subunit from Pyrococcus furiosus, PfTrpB, for ncAA synthase activity in the absence of its native partner protein PfTrpA. However, the precise mechanism by which mutation activated TrpB to afford a stand-alone catalyst remained enigmatic. Here, we show that directed evolution caused a gradual change in the rate-limiting step of the catalytic cycle. Concomitantly, the steady-state distribution of the intermediates shifts to favor covalently bound Trp adducts, which have increased thermodynamic stability. The biochemical properties of these evolved, stand-alone TrpBs converge on those induced in the native system by allosteric activation. High-resolution crystal structures of the wild-type enzyme, an intermediate in the lineage, and the final variant, encompassing five distinct chemical states, show that activating mutations have only minor structural effects on their immediate environment. Instead, mutation stabilizes the large-scale motion of a subdomain to favor an otherwise transiently populated closed conformational state. This increase in stability enabled the first structural description of Trp covalently bound in a catalytically active TrpB, confirming key features of catalysis. These data combine to show that sophisticated models of allostery are not a prerequisite to recapitulating its complex effects via directed evolution, opening the way to engineering stand-alone versions of diverse allosteric enzymes.
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Affiliation(s)
- Andrew R. Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Paul van Roye
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Jackson K.B. Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, Zurich 8093, Switzerland
| | - Remkes A. Scheele
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Michael Herger
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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31
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Carvalho ATP, Dourado DFAR, Skvortsov T, de Abreu M, Ferguson LJ, Quinn DJ, Moody TS, Huang M. Spatial requirement for PAMO for transformation of non-native linear substrates. Phys Chem Chem Phys 2018; 20:2558-2570. [PMID: 29318252 DOI: 10.1039/c7cp07172h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phenylacetone monooxygenase is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenases family, and therefore it is an ideal candidate for the synthesis of industrially relevant ester or lactone compounds. However, its limited substrate scope has largely limited its industrial applications. Linear substrates are interesting from an industrial point of view, it is thus necessary to identify the essential spatial requirement for achieving high conversions for non-native linear substrates. Here using molecular dynamics simulations, we compared the conversion of a non-native linear substrate 2-octanone and the native substrate phenylacetone, catalyzed by the WT enzyme and a quadruple variant P253F/G254A/R258M/L443F that exhibits significantly improved activity towards 2-octanone. We uncovered that a remarkable movement of L289 is crucial for a reshaping of the active site of the quadruple variant so as to prevent the aliphatic substrate from moving away from the C4a-peroxyflavin, thus enabling it to keep a catalytically relevant pose during the oxygenation process. By performing steady-state kinetic analysis of two single-mutation variants at position 258, we further validated that the L289 reposition is attributed to the combined effect of quadruple mutations. In order to further explore the substrate scope of PAMO we also studied the binding of cyclopentanone and 2-phenylcyclohexanone, which are the typical substrates of CPMO in group I and CHMO in group III, respectively. Our study provides fundamental atomic-level insights in rational engineering of PAMO for wide applications in industrial biocatalysis, in particular, in the biotransformation of long-chain aliphatic oils into potential biodiesels.
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Affiliation(s)
- Alexandra T P Carvalho
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
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32
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Carvalho ATP, Dourado DFAR, Skvortsov T, de Abreu M, Ferguson LJ, Quinn DJ, Moody TS, Huang M. Catalytic mechanism of phenylacetone monooxygenases for non-native linear substrates. Phys Chem Chem Phys 2018; 19:26851-26861. [PMID: 28951930 DOI: 10.1039/c7cp03640j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Phenylacetone monooxygenase (PAMO) is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenase family, and therefore it is an ideal candidate for the synthesis of industrially relevant compounds. However, its limited substrate scope has largely limited its industrial applications. In the present work, we provide, for the first time, the catalytic mechanism of PAMO for the native substrate phenylacetone as well as for a linear non-native substrate 2-octanone, using molecular dynamics simulations, quantum mechanics and quantum mechanics/molecular mechanics calculations. We provide a theoretical basis for the preference of the enzyme for the native aromatic substrate over non-native linear substrates. Our study provides fundamental atomic-level insights that can be employed in the rational engineering of PAMO for wide applications in industrial biocatalysis, in particular, in the biotransformation of long-chain aliphatic oils into potential biodiesels.
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Affiliation(s)
- Alexandra T P Carvalho
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
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33
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Affiliation(s)
- Srivatsan Raman
- Department of Biochemistry
and Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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34
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Balke K, Beier A, Bornscheuer UT. Hot spots for the protein engineering of Baeyer-Villiger monooxygenases. Biotechnol Adv 2018; 36:247-263. [DOI: 10.1016/j.biotechadv.2017.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
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Abstract
Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany.
- Biosyntia ApS, 2100, Copenhagen, Denmark.
| | - Matteo Ferla
- Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany
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36
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Department of Chemistry; Philipps-University; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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Willetts A, Kelly D. Reply to the Comment by Littlechild and Isupov. Microorganisms 2017; 5:microorganisms5030055. [PMID: 28878173 PMCID: PMC5620646 DOI: 10.3390/microorganisms5030055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 11/16/2022] Open
Abstract
I thank Drs. Littlechild and Isupov for their recent comments, which are considered below. Before addressing these specifically, their correspondence raises two more general issues which require initial clarification.[...].
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Affiliation(s)
- Andrew Willetts
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, UK.
| | - David Kelly
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
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38
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Bisagni S, Abolhalaj M, de Brevern AG, Rebehmed J, Hatti-Kaul R, Mamo G. Enhancing the Activity of a Dietzia
sp. D5 Baeyer-Villiger Monooxygenase towards Cyclohexanone by Saturation Mutagenesis. ChemistrySelect 2017. [DOI: 10.1002/slct.201701212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Serena Bisagni
- Biotechnology, Department of Chemistry; Centre for Chemistry and Chemical Engineering; Lund University; Box 124 SE-221 00 Lund Sweden
- Johnson Matthey; Cambridge Science Park 28 CB4 0FP Cambridge United Kingdom
| | - Milad Abolhalaj
- Department of Immunotechnology; Medicon Village; Scheelevägen 2 22100 Lund Sweden
| | - Alexandre G. de Brevern
- Inserm U1134; Paris France
- Université Paris Diderot; Sorbonne, Paris Cité, UMR_S 1134; Paris France
- Institut National de la Transfusion Sanguine; Paris France
- Laboratory of Excellence GR-Ex; Paris France
| | - Joseph Rebehmed
- Inserm U1134; Paris France
- Université Paris Diderot; Sorbonne, Paris Cité, UMR_S 1134; Paris France
- Institut National de la Transfusion Sanguine; Paris France
- Laboratory of Excellence GR-Ex; Paris France
- Department of Computer Science and Mathematics; Lebanese American University; Byblos 1 h401 2010 Lebanon
| | - Rajni Hatti-Kaul
- Biotechnology, Department of Chemistry; Centre for Chemistry and Chemical Engineering; Lund University; Box 124 SE-221 00 Lund Sweden
| | - Gashaw Mamo
- Biotechnology, Department of Chemistry; Centre for Chemistry and Chemical Engineering; Lund University; Box 124 SE-221 00 Lund Sweden
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39
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Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Development of Halogenase Enzymes for Use in Synthesis. Chem Rev 2017; 118:232-269. [PMID: 28466644 DOI: 10.1021/acs.chemrev.7b00032] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.
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Affiliation(s)
- Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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40
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Acevedo JP, Reetz MT, Asenjo JA, Parra LP. One-step combined focused epPCR and saturation mutagenesis for thermostability evolution of a new cold-active xylanase. Enzyme Microb Technol 2017; 100:60-70. [PMID: 28284313 DOI: 10.1016/j.enzmictec.2017.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/25/2017] [Accepted: 02/09/2017] [Indexed: 11/17/2022]
Abstract
Enzymes active at low temperature are of great interest for industrial bioprocesses due to their high efficiency at a low energy cost. One of the particularities of naturally evolved cold-active enzymes is their increased enzymatic activity at low temperature, however the low thermostability presented in this type of enzymes is still a major drawback for their application in biocatalysis. Directed evolution of cold-adapted enzymes to a more thermostable version, appears as an attractive strategy to fulfill the stability and activity requirements for the industry. This paper describes the recombinant expression and characterization of a new and highly active cold-adapted xylanase from the GH-family 10 (Xyl-L), and the use of a novel one step combined directed evolution technique that comprises saturation mutagenesis and focused epPCR as a feasible semi-rational strategy to improve the thermostability. The Xyl-L enzyme was cloned from a marine-Antarctic bacterium, Psychrobacter sp. strain 2-17, recombinantly expressed in E. coli strain BL21(DE3) and characterized enzymatically. Molecular dynamic simulations using a homology model of the catalytic domain of Xyl-L were performed to detect flexible regions and residues, which are considered to be the possible structural elements that define the thermolability of this enzyme. Mutagenic libraries were designed in order to stabilize the protein introducing mutations in some of the flexible regions and residues identified. Twelve positive mutant clones were found to improve the T5015 value of the enzyme, in some cases without affecting the activity at 25°C. The best mutant showed a 4.3°C increase in its T5015. The efficiency of the directed evolution approach can also be expected to work in the protein engineering of stereoselectivity.
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Affiliation(s)
- Juan Pablo Acevedo
- Facultad de Medicina y Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, San Carlos de Apoquindo, 2200 Santiago, Chile
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, 45070 Mülheim, Germany; Chemistry Department, Philipps-University, 35032 Marburg, Germany
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef, 851 Santiago, Chile
| | - Loreto P Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna, 4860 Santiago, Chile; Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna, 4860 Santiago, Chile.
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41
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Li G, Fürst MJLJ, Mansouri HR, Ressmann AK, Ilie A, Rudroff F, Mihovilovic MD, Fraaije MW, Reetz MT. Manipulating the stereoselectivity of the thermostable Baeyer–Villiger monooxygenase TmCHMO by directed evolution. Org Biomol Chem 2017; 15:9824-9829. [DOI: 10.1039/c7ob02692g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The thermostable Baeyer–Villiger monooxygenase TmCHMO and evolved mutants are viable catalysts in stereoselective reactions of structurally different ketones.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung
- Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
- Philipps-Universität
| | | | | | - Anna K. Ressmann
- Institute of Applied Synthetic Chemistry
- TU Wien
- 1060 Vienna
- Austria
| | - Adriana Ilie
- Max-Planck-Institut für Kohlenforschung
- Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
- Philipps-Universität
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry
- TU Wien
- 1060 Vienna
- Austria
| | | | - Marco W. Fraaije
- Molecular Enzymology Group
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung
- Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
- Philipps-Universität
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42
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Chen K, Wu S, Zhu L, Zhang C, Xiang W, Deng Z, Ikeda H, Cane DE, Zhu D. Substitution of a Single Amino Acid Reverses the Regiospecificity of the Baeyer-Villiger Monooxygenase PntE in the Biosynthesis of the Antibiotic Pentalenolactone. Biochemistry 2016; 55:6696-6704. [PMID: 27933799 DOI: 10.1021/acs.biochem.6b01040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the biosynthesis of pentalenolactone (1), PenE and PntE, orthologous proteins from Streptomyces exfoliatus and S. arenae, respectively, catalyze the flavin-dependent Baeyer-Villiger oxidation of 1-deoxy-11-oxopentalenic acid (4) to the lactone pentalenolactone D (5), in which the less-substituted methylene carbon has migrated. By contrast, the paralogous PtlE enzyme from S. avermitilis catalyzes the oxidation of 4 to neopentalenolactone D (6), in which the more substituted methane substitution has undergone migration. We report the design and analysis of 13 single and multiple mutants of PntE mutants to identify the key amino acids that contribute to the regiospecificity of these two classes of Baeyer-Villiger monooxygenases. The L185S mutation in PntE reversed the observed regiospecificity of PntE such that all recombinant PntE mutants harboring this L185S mutation acquired the characteristic regiospecificity of PtlE, catalyzing the conversion of 4 to 6 as the major product. The recombinant PntE mutant harboring R484L exhibited reduced regiospecificity, generating a mixture of lactones containing more than 17% of 6. These in vitro results were corroborated by analysis of the complementation of the S. avermitilis ΔptlED double deletion mutant with pntE mutants, such that pntE mutants harboring L185S produced 6 as the major product, whereas complemention of the ΔptlED deletion mutant with pntE mutants carrying the R484L mutation gave 6 as more than 33% of the total lactone product mixture.
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Affiliation(s)
- Ke Chen
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Shiwen Wu
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Lu Zhu
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Chengde Zhang
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University , Harbin, Heilongjiang Province 150030, China
| | - Zixin Deng
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato, Sagamihara, Minami-ku, Kanagawa 252-0373, Japan
| | - David E Cane
- Department of Chemistry, Box H, Brown University , Providence, Rhode Island 02912-9108, United States
| | - Dongqing Zhu
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
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43
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Facilitating the Evolution of Esterase Activity from a Promiscuous Enzyme (Mhg) with Catalytic Functions of Amide Hydrolysis and Carboxylic Acid Perhydrolysis by Engineering the Substrate Entrance Tunnel. Appl Environ Microbiol 2016; 82:6748-6756. [PMID: 27613682 DOI: 10.1128/aem.01817-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/04/2016] [Indexed: 11/20/2022] Open
Abstract
Promiscuous enzymes are generally considered to be starting points in the evolution of offspring enzymes with more specific or even novel catalytic activities, which is the molecular basis of producing new biological functions. Mhg, a typical α/β fold hydrolase, was previously reported to have both γ-lactamase and perhydrolase activities. However, despite having high structural similarity to and sharing an identical catalytic triad with an extensively studied esterase from Pseudomonas fluorescens, this enzyme did not show any esterase activity. Molecular docking and sequence analysis suggested a possible role for the entry of the binding pocket in blocking the entrance tunnel, preventing the ester compounds from entering into the pocket. By engineering the entrance tunnel with only one or two amino acid substitutions, we successfully obtained five esterase variants of Mhg. The variants exhibited a very broad substrate acceptance, hydrolyzing not only the classical p-nitrophenol esters but also various types of chiral esters, which are widely used as drug intermediates. Site 233 at the entrance tunnel of Mhg was found to play a pivotal role in modulating the three catalytic activities by adjusting the size and shape of the tunnel, with different amino acid substitutions at this site facilitating different activities. Remarkably, the variant with the L233G mutation was a very specific esterase without any γ-lactamase and perhydrolase activities. Considering the amino acid conservation and differentiation, this site could be a key target for future protein engineering. In addition, we demonstrate that engineering the entrance tunnel is an efficient strategy to regulate enzyme catalytic capabilities. IMPORTANCE Promiscuous enzymes can act as starting points in the evolution of novel catalytic activities, thus providing a molecular basis for the production of new biological functions. In this study, we identified a critical amino acid residue (Leu233) at the entry of the substrate tunnel of a promiscuous enzyme, Mhg. We found that substitution of this residue with smaller amino acids such as Gly, Ala, Ser, or Pro endowed the enzyme with novel esterase activity. Different amino acids at this site can facilitate different catalytic activities. These findings exhibited universal significance in this subset of α/β fold hydrolases, including Mhg. Furthermore, we demonstrate that engineering the entrance tunnel is an efficient strategy to evolve new enzyme catalytic capabilities. Our study has important implications for the regulation of enzyme catalytic promiscuity and development of protein engineering methodologies.
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44
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Reetz MT. What are the Limitations of Enzymes in Synthetic Organic Chemistry? CHEM REC 2016; 16:2449-2459. [DOI: 10.1002/tcr.201600040] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Manfred T. Reetz
- Fachbereich Chemie (15) Philipps-Universität Marburg Hans-Meerwein Straße; 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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45
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Bhowmick A, Sharma SC, Honma H, Head-Gordon T. The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70. Phys Chem Chem Phys 2016; 18:19386-96. [DOI: 10.1039/c6cp03622h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Side chain entropy and mutual entropy information between residue pairs have been calculated for two de novo designed Kemp eliminase enzymes, KE07 and KE70, and for their most improved versions at the end of laboratory directed evolution (LDE).
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Affiliation(s)
- Asmit Bhowmick
- Department of Chemical and Biomolecular Engineering
- University of California Berkeley
- Berkeley
- USA
| | - Sudhir C. Sharma
- Department of Chemistry
- University of California Berkeley
- Berkeley
- USA
| | - Hallie Honma
- Department of Bioengineering, University of California Berkeley
- Berkeley
- USA
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering
- University of California Berkeley
- Berkeley
- USA
- Department of Chemistry
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46
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Tobin PH, Richards DH, Callender RA, Wilson CJ. Protein engineering: a new frontier for biological therapeutics. Curr Drug Metab 2015; 15:743-56. [PMID: 25495737 DOI: 10.2174/1389200216666141208151524] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/27/2014] [Accepted: 12/07/2014] [Indexed: 12/14/2022]
Abstract
Protein engineering holds the potential to transform the metabolic drug landscape through the development of smart, stimulusresponsive drug systems. Protein therapeutics are a rapidly expanding segment of Food and Drug Administration approved drugs that will improve clinical outcomes over the long run. Engineering of protein therapeutics is still in its infancy, but recent general advances in protein engineering capabilities are being leveraged to yield improved control over both pharmacokinetics and pharmacodynamics. Stimulus- responsive protein therapeutics are drugs which have been designed to be metabolized under targeted conditions. Protein engineering is being utilized to develop tailored smart therapeutics with biochemical logic. This review focuses on applications of targeted drug neutralization, stimulus-responsive engineered protein prodrugs, and emerging multicomponent smart drug systems (e.g., antibody-drug conjugates, responsive engineered zymogens, prospective biochemical logic smart drug systems, drug buffers, and network medicine applications).
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Affiliation(s)
| | | | | | - Corey J Wilson
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, USA.
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47
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Tiberti M, Invernizzi G, Papaleo E. (Dis)similarity Index To Compare Correlated Motions in Molecular Simulations. J Chem Theory Comput 2015; 11:4404-14. [PMID: 26575932 DOI: 10.1021/acs.jctc.5b00512] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulations are widely used to complement or guide experimental studies in the characterization of protein dynamics, thanks to improvements in force-field accuracy, along with in the software and hardware to sample the conformational landscape of proteins. Among the different applications of MD simulations, the study of correlated motions is largely employed for different purposes. Several metrics have been developed to describe correlated motions in the MD ensemble, such as methods based on Pearson Correlation or Mutual Information. Cross-correlation analysis of MD trajectories is indeed appealing not only to identify residues characterized by coupled fluctuations in protein structures but also since it can be used to extrapolate motions along directions in which major conformational changes should occur, for example on longer time scales than the ones that are actually simulated. Nevertheless, most of the MD studies employ average correlation maps and mostly in a qualitative way, even when different systems or different replicates of the same system are compared. The broad application of correlation metrics in the analysis of MD simulations, especially for comparative purposes, requires a step forward toward more quantitative and accurate comparisons. We thus here employed a simple but effective index, which is based on a normalized Frobenius norm of the differences between protein correlation maps, to compare correlated motions. We applied this index for a quantitative comparison of correlated motions from MD simulations of seven proteins of different size and fold. We also employed the index to assess the robustness of correlation description when multi-replicate MD simulations of a same system are used, and we compared our index to metrics for comparison of structural ensembles such as Root Mean Square Inner Product and the Bhattacharyya Coefficient.
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Affiliation(s)
- Matteo Tiberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Gaetano Invernizzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
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48
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Holtmann D, Fraaije MW, Arends IWCE, Opperman DJ, Hollmann F. The taming of oxygen: biocatalytic oxyfunctionalisations. Chem Commun (Camb) 2015; 50:13180-200. [PMID: 24902635 DOI: 10.1039/c3cc49747j] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scope and limitations of oxygenases as catalysts for preparative organic synthesis is discussed.
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Affiliation(s)
- Dirk Holtmann
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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49
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Parra LP, Acevedo JP, Reetz MT. Directed evolution of phenylacetone monooxygenase as an active catalyst for the Baeyer-Villiger conversion of cyclohexanone to caprolactone. Biotechnol Bioeng 2015; 112:1354-64. [PMID: 25675885 DOI: 10.1002/bit.25564] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/05/2015] [Indexed: 01/10/2023]
Abstract
Phenylacetone monooxygenase (PAMO) is an exceptionally robust Baeyer-Villiger monooxygenase, which makes it ideal for potential industrial applications. However, its substrate scope is limited, unreactive cyclohexanone being a prominent example. Such a limitation is unfortunate, because this particular transformation in an ecologically viable manner would be highly desirable, the lactone and the respective lactam being of considerable interest as monomers in polymer science. We have applied directed evolution in search of an active mutant for this valuable C-C activating reaction. Using iterative saturation mutagenesis (ISM), several active mutants were evolved, with only a minimal trade-off in terms of stability. The best mutants allow for quantitative conversion of 2 mM cyclohexanone within 1 h reaction time. In order to circumvent the NADP(+) regeneration problem, whole E. coli resting cells were successfully applied. Molecular dynamics simulations and induced fit docking throw light on the origin of enhanced PAMO activity. The PAMO mutants constitute ideal starting points for future directed evolution optimization necessary for an industrial process.
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Affiliation(s)
- Loreto P Parra
- Department of Synthetic Organic Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fachbereich Chemie Philipps-Universität Marburg, Marburg, Germany.,Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan P Acevedo
- Department of Synthetic Organic Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fachbereich Chemie Philipps-Universität Marburg, Marburg, Germany.,Facultad de Medicina y Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, Santiago, Chile
| | - Manfred T Reetz
- Department of Synthetic Organic Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany. .,Fachbereich Chemie Philipps-Universität Marburg, Marburg, Germany.
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Makhlynets OV, Raymond EA, Korendovych IV. Design of allosterically regulated protein catalysts. Biochemistry 2015; 54:1444-56. [PMID: 25642601 DOI: 10.1021/bi5015248] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Activity of allosteric protein catalysts is regulated by an external stimulus, such as protein or small molecule binding, light activation, pH change, etc., at a location away from the active site of the enzyme. Since its original introduction in 1961, the concept of allosteric regulation has undergone substantial expansion, and many, if not most, enzymes have been shown to possess some degree of allosteric regulation. The ability to create new catalysts that can be turned on and off using allosteric interactions would greatly expand the chemical biology toolbox and will allow for detection of environmental pollutants and disease biomarkers and facilitate studies of cellular processes and metal homeostasis. Thus, design of allosterically regulated protein catalysts represents an actively growing area of research. In this paper, we describe various approaches to achieving regulation of catalysis.
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Affiliation(s)
- Olga V Makhlynets
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
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