1
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Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabrière E, Daudé D, Elias MH. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity. JACS AU 2024; 4:1941-1953. [PMID: 38818068 PMCID: PMC11134384 DOI: 10.1021/jacsau.4c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/01/2024]
Abstract
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver of the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being >1000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, and some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops and changes to their conformations, as revealed by a suite of crystal structures. This suggests that a specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining the enzyme activity profile.
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Affiliation(s)
| | - Raphaël Billot
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
| | - Amir Shimon
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Nathan Hoekstra
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Céline Bergonzi
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Anthony Jenks
- Department
of Biochemistry, Molecular Biology and Biophysics & Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Eric Chabrière
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
- Aix
Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - David Daudé
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
| | - Mikael H. Elias
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
- Department
of Biochemistry, Molecular Biology and Biophysics & Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
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2
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Williams TL, Taily IM, Hatton L, Berezin AA, Wu YL, Moliner V, Świderek K, Tsai YH, Luk LYP. Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion. Angew Chem Int Ed Engl 2024; 63:e202403098. [PMID: 38545954 DOI: 10.1002/anie.202403098] [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: 02/13/2024] [Indexed: 04/20/2024]
Abstract
Secondary amines, due to their reactivity, can transform protein templates into catalytically active entities, accelerating the development of artificial enzymes. However, existing methods, predominantly reliant on modified ligands or N-terminal prolines, impose significant limitations on template selection. In this study, genetic code expansion was used to break this boundary, enabling secondary amines to be incorporated into alternative proteins and positions of choice. Pyrrolysine analogues carrying different secondary amines could be incorporated into superfolder green fluorescent protein (sfGFP), multidrug-binding LmrR and nucleotide-binding dihydrofolate reductase (DHFR). Notably, the analogue containing a D-proline moiety demonstrated both proteolytic stability and catalytic activity, conferring LmrR and DHFR with the desired transfer hydrogenation activity. While the LmrR variants were confined to the biomimetic 1-benzyl-1,4-dihydronicotinamide (BNAH) as the hydride source, the optimal DHFR variant favorably used the pro-R hydride from NADPH for stereoselective reactions (e.r. up to 92 : 8), highlighting that a switch of protein template could broaden the nucleophile option for catalysis. Owing to the cofactor compatibility, the DHFR-based secondary amine catalysis could be integrated into an enzymatic recycling scheme. This established method shows substantial potential in enzyme design, applicable from studies on enzyme evolution to the development of new biocatalysts.
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Affiliation(s)
- Thomas L Williams
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Irshad M Taily
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Lewis Hatton
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Andrey A Berezin
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Yi-Lin Wu
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Gaoke International Innovation Center, Guangming District, 518132, Shenzhen, Guangdong, China
| | - Louis Y P Luk
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
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3
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Thomas MG, Jaber Sathik Rifayee SB, Chaturvedi SS, Gorantla KR, White W, Wildey J, Schofield CJ, Christov CZ. The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A. Inorg Chem 2024. [PMID: 38781256 DOI: 10.1021/acs.inorgchem.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.
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Affiliation(s)
| | | | | | | | | | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12, Mansfield Road, Oxford OX1 5JJ, U.K
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4
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Bessoni Kosctiuk J, Ribeiro Neto ME, Alcoforado Pereira G, Krieger N, Zambelli Mezalira D, Pilissão C. A Multicomponent Mannich Reaction Catalyzed by Hydrolases Immobilized on Titanate Nanotubes. Chempluschem 2024; 89:e202300698. [PMID: 38242852 DOI: 10.1002/cplu.202300698] [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: 11/28/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/21/2024]
Abstract
This study presents an innovative method for synthesizing β-amino carbonylated compounds, specifically 2-[phenyl(phenylamino)methyl] cyclohexanone, achieving high conversions and diastereomeric ratios. Using trypsin or α-chymotrypsin in both free and immobilized forms on titanate nanotubes (NtsTi), synthesized through alkaline hydrothermal methods, successful immobilization yields were attained. Notably, α-chymotrypsin, when free, displayed a diastereoselective synthesis of the anti-isomer with 97 % conversion and 16 : 84 (syn : anti) diastereomeric ratio, which slightly decreased upon immobilization on NtsTi. Trypsin, in its free form, exhibited diastereoselective recognition of the syn-isomer, while immobilization on NtsTi (trypsin/NtsTi) led to an inversion of diastereomeric ratio. Both trypsin/NtsTi and α-chymotrypsin/NtsTi demonstrated significant catalytic efficiency over five cycles. In conclusion, NtsTi serves as an effective support for trypsin and α-chymotrypsin immobilization, presenting promising prospects for diastereoselective synthesis and potential industrial applications. Furthermore, it offers promising prospects for the diastereoselective synthesis of 2-[phenyl(phenylamino)methyl] cyclohexanone through multicomponent Mannich reaction and future industrial application.
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Affiliation(s)
- Juliane Bessoni Kosctiuk
- Department of Chemistry and Biology, Federal University Technological of Paraná, 81280-340, Curitiba, PR, Brazil
| | - Matheus Enrique Ribeiro Neto
- Department of Chemistry and Biology, Federal University Technological of Paraná, 81280-340, Curitiba, PR, Brazil
| | - Gabriela Alcoforado Pereira
- Department of Chemistry and Biology, Federal University Technological of Paraná, 81280-340, Curitiba, PR, Brazil
| | - Nadia Krieger
- Department of Chemistry, Federal University of Paraná, 81531-980, Curitiba, PR, Brazil
| | | | - Cristiane Pilissão
- Department of Chemistry and Biology, Federal University Technological of Paraná, 81280-340, Curitiba, PR, Brazil
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5
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Hashemi S, Laitinen R, Nikoloski Z. Models and molecular mechanisms for trade-offs in the context of metabolism. Mol Ecol 2024; 33:e16879. [PMID: 36773330 DOI: 10.1111/mec.16879] [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: 08/10/2022] [Revised: 01/19/2023] [Accepted: 02/07/2023] [Indexed: 02/13/2023]
Abstract
Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in the evolution of organisms. Metabolic models with different levels of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) the kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) the rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into the mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relationship of metabolic trade-offs to the classical black box Y-model that provides a conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.
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Affiliation(s)
- Seirana Hashemi
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Roosa Laitinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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6
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Longwitz L, Leveson-Gower RB, Rozeboom HJ, Thunnissen AMWH, Roelfes G. Boron catalysis in a designer enzyme. Nature 2024; 629:824-829. [PMID: 38720081 DOI: 10.1038/s41586-024-07391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/05/2024] [Indexed: 05/24/2024]
Abstract
Enzymes play an increasingly important role in improving the benignity and efficiency of chemical production, yet the diversity of their applications lags heavily behind chemical catalysts as a result of the relatively narrow range of reaction mechanisms of enzymes. The creation of enzymes containing non-biological functionalities facilitates reaction mechanisms outside nature's canon and paves the way towards fully programmable biocatalysis1-3. Here we present a completely genetically encoded boronic-acid-containing designer enzyme with organocatalytic reactivity not achievable with natural or engineered biocatalysts4,5. This boron enzyme catalyses the kinetic resolution of hydroxyketones by oxime formation, in which crucial interactions with the protein scaffold assist in the catalysis. A directed evolution campaign led to a variant with natural-enzyme-like enantioselectivities for several different substrates. The unique activation mode of the boron enzyme was confirmed using X-ray crystallography, high-resolution mass spectrometry (HRMS) and 11B NMR spectroscopy. Our study demonstrates that genetic-code expansion can be used to create evolvable enantioselective enzymes that rely on xenobiotic catalytic moieties such as boronic acids and access reaction mechanisms not reachable through catalytic promiscuity of natural or engineered enzymes.
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Affiliation(s)
- Lars Longwitz
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | | | - Henriëtte J Rozeboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands.
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7
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Westarp S, Brandt F, Neumair L, Betz C, Dagane A, Kemper S, Jacob CR, Neubauer P, Kurreck A, Kaspar F. Nucleoside Phosphorylases make N7-xanthosine. Nat Commun 2024; 15:3625. [PMID: 38684649 PMCID: PMC11058261 DOI: 10.1038/s41467-024-47287-4] [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: 10/23/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Modern, highly evolved nucleoside-processing enzymes are known to exhibit perfect regioselectivity over the glycosylation of purine nucleobases at N9. We herein report an exception to this paradigm. Wild-type nucleoside phosphorylases also furnish N7-xanthosine, a "non-native" ribosylation regioisomer of xanthosine. This unusual nucleoside possesses several atypical physicochemical properties such as redshifted absorption spectra, a high equilibrium constant of phosphorolysis and low acidity. Ultimately, the biosynthesis of this previously unknown natural product illustrates how even highly evolved, essential enzymes from primary metabolism are imperfect catalysts.
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Affiliation(s)
- Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Lena Neumair
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Christina Betz
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Amin Dagane
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany.
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
| | - Felix Kaspar
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.
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8
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Wu L, Lin H, Cao X, Tong Q, Yang F, Miao Y, Ye D, Fan Q. Bioorthogonal Cu Single-Atom Nanozyme for Synergistic Nanocatalytic Therapy, Photothermal Therapy, Cuproptosis and Immunotherapy. Angew Chem Int Ed Engl 2024:e202405937. [PMID: 38654446 DOI: 10.1002/anie.202405937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Single-atom nanozymes (SAzymes) with atomically dispersed active sites are potential substitutes for natural enzymes. A systematic study of its multiple functions can in-depth understand SAzymes's nature, which remains elusive. Here, we develop a novel ultrafast synthesis of sputtered SAzymes by in situ bombarding-embedding technique. Using this method, sputtered copper (Cu) SAzymes (CuSA) is developed with unreported unique planar Cu-C3 coordinated configuration. To enhance the tumor-specific targeting, we employ a bioorthogonal approach to engineer CuSA, denoted as CuSACO. CuSACO not only exhibits minimal off-target toxicity but also possesses exceptional ultrahigh catalase-, oxidase-, peroxidase-like multienzyme activities, resulting in reactive oxygen species (ROS) storm generation for effective tumor destruction. Surprisingly, CuSACO can release Cu ions in the presence of glutathione (GSH) to induce cuproptosis, enhancing the tumor treatment efficacy. Notably, CuSACO's remarkable photothermal properties enables precise photothermal therapy (PTT) on tumors. This, combined with nanozyme catalytic activities, cuproptosis and immunotherapy, efficiently inhibiting the growth of orthotopic breast tumors and gliomas, and lung metastasis. Our research highlights the potential of CuSACO as an innovative strategy to utilize multiple mechanism to enhance tumor therapeutic efficacy, broadening the exploration and development of enzyme-like behavior and physiological mechanism of action of SAzymes.
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Affiliation(s)
- Luyan Wu
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Huihui Lin
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, 627833, Singapore
- Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
| | - Xiang Cao
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), School of Chemistry and Life Sciences, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Qiang Tong
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Fangqi Yang
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Yinxing Miao
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Deju Ye
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Quli Fan
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
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9
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Guo X, Ong WM, Zhao HP, Lai CY. Enzyme-induced reactive oxygen species trigger oxidative degradation of sulfamethoxazole within a methanotrophic biofilm. WATER RESEARCH 2024; 253:121330. [PMID: 38387268 DOI: 10.1016/j.watres.2024.121330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Although microorganisms carrying copper-containing membrane-bound monooxygenase (CuMMOs), such as particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO), have been extensively documented for their capability to degrade organic micropollutants (OMPs), the underlying reactive mechanism remains elusive. In this study, we for the first time demonstrate biogenic reactive oxygen species (ROS) play important roles in the degradation of sulfamethoxazole (SMX), a representative OMP, within a methane-fed biofilm. Highly-efficient and consistent SMX biodegradation was achieved in a CH4-based membrane biofilm reactor (MBfR), manifesting a remarkable SMX removal rate of 1210.6 ± 39.0 μg·L-1·d-1. Enzyme inhibition and ROS clearance experiments confirmed the significant contribution of ROS, which were generated through the catalytic reaction of pMMO and AMO enzymes, in facilitating SMX degradation. Through a combination of density functional theory (DFT) calculations, electron paramagnetic resonance (EPR) analysis, and transformation product detection, we elucidated that the ROS primarily targeted the aniline group in the SMX molecule, inducing the formation of aromatic radicals and its progressive mineralization. In contrast, the isoxazole-ring was not susceptible to electrophilic ROS attacks, leading to accumulation of 3-amino-5-methylisoxazole (3A5MI). Furthermore, microbiological analysis suggested Methylosarcina (a methanotroph) and Candidatus Nitrosotenuis (an ammonia-oxidizing archaea) collaborated as the SMX degraders, who carried highly conserved and expressed CuMMOs (pMMO and AMO) for ROS generation, thereby triggering the oxidative degradation of SMX. This study deciphers SMX biodegradation through a fresh perspective of free radical chemistry, and concurrently providing a theoretical framework for the advancement of environmental biotechnologies aimed at OMP removal.
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Affiliation(s)
- Xu Guo
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Weng Mun Ong
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Chun-Yu Lai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058.
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10
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Thorpe T, Marshall JR, Turner NJ. Multifunctional Biocatalysts for Organic Synthesis. J Am Chem Soc 2024; 146:7876-7884. [PMID: 38489244 PMCID: PMC10979396 DOI: 10.1021/jacs.3c09542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
Biocatalysis is becoming an indispensable tool in organic synthesis due to high enzymatic catalytic efficiency as well as exquisite chemo- and stereoselectivity. Some biocatalysts display great promiscuity including a broad substrate scope as well as the ability to catalyze more than one type of transformation. These promiscuous activities have been applied individually to efficiently access numerous valuable target molecules. However, systems in which enzymes possessing multiple different catalytic activities are applied in the synthesis are less well developed. Such multifunctional biocatalysts (MFBs) would simplify chemical synthesis by reducing the number of operational steps and enzyme count, as well as simplifying the sequence space that needs to be engineered to develop an efficient biocatalyst. In this Perspective, we highlight recently reported MFBs focusing on their synthetic utility and mechanism. We also offer insight into their origin as well as comment on potential strategies for their discovery and engineering.
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Affiliation(s)
- Thomas
W. Thorpe
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
| | - James R. Marshall
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
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11
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Yan W, Li X, Zhao D, Xie M, Li T, Qian L, Ye C, Shi T, Wu L, Wang Y. Advanced strategies in high-throughput droplet screening for enzyme engineering. Biosens Bioelectron 2024; 248:115972. [PMID: 38171222 DOI: 10.1016/j.bios.2023.115972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/05/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024]
Abstract
Enzymes, as biocatalysts, play a cumulatively important role in environmental purification and industrial production of chemicals and pharmaceuticals. However, natural enzymes are limited by their physiological properties in practice, which need to be modified driven by requirements. Screening and isolating certain enzyme variants or ideal industrial strains with high yielding of target product enzymes is one of the main directions of enzyme engineering research. Droplet-based high-throughput screening (DHTS) technology employs massive monodisperse emulsion droplets as microreactors to achieve single strain encapsulation, as well as continuous monitoring for the inside mutant library. It can effectively sort out strains or enzymes with desired characteristics, offering a throughput of 108 events per hour. Much of the early literature focused on screening various engineered strains or designing signalling sorting strategies based on DHTS technology. However, the field of enzyme engineering lacks a comprehensive overview of advanced methods for microfluidic droplets and their cutting-edge developments in generation and manipulation. This review emphasizes the advanced strategies and frontiers of microfluidic droplet generation and manipulation facilitating enzyme engineering development. We also introduce design for various screening signals that cooperate with DHTS and devote to enzyme engineering.
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Affiliation(s)
- Wenxin Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Xiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Danshan Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Meng Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Ting Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Lu Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Ministry of Education Key Laboratory of NSLSCS, Nanjing Normal University, Nanjing 210046, China.
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Food Laboratory of Zhongyuan, Luohe, 462300, Henan, China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
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12
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Hansen AL, Theisen FF, Crehuet R, Marcos E, Aghajari N, Willemoës M. Carving out a Glycoside Hydrolase Active Site for Incorporation into a New Protein Scaffold Using Deep Network Hallucination. ACS Synth Biol 2024; 13:862-875. [PMID: 38357862 PMCID: PMC10949244 DOI: 10.1021/acssynbio.3c00674] [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: 11/08/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Enzymes are indispensable biocatalysts for numerous industrial applications, yet stability, selectivity, and restricted substrate recognition present limitations for their use. Despite the importance of enzyme engineering in overcoming these limitations, success is often challenged by the intricate architecture of enzymes derived from natural sources. Recent advances in computational methods have enabled the de novo design of simplified scaffolds with specific functional sites. Such scaffolds may be advantageous as platforms for enzyme engineering. Here, we present a strategy for the de novo design of a simplified scaffold of an endo-α-N-acetylgalactosaminidase active site, a glycoside hydrolase from the GH101 enzyme family. Using a combination of trRosetta hallucination, iterative cycles of deep-learning-based structure prediction, and ProteinMPNN sequence design, we designed proteins with 290 amino acids incorporating the active site while reducing the molecular weight by over 100 kDa compared to the initial endo-α-N-acetylgalactosaminidase. Of 11 tested designs, six were expressed as soluble monomers, displaying similar or increased thermostabilities compared to the natural enzyme. Despite lacking detectable enzymatic activity, the experimentally determined crystal structures of a representative design closely matched the design with a root-mean-square deviation of 1.0 Å, with most catalytically important side chains within 2.0 Å. The results highlight the potential of scaffold hallucination in designing proteins that may serve as a foundation for subsequent enzyme engineering.
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Affiliation(s)
- Anders Lønstrup Hansen
- The
Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular
Sciences, Department of Biology, University
of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Frederik Friis Theisen
- The
Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular
Sciences, Department of Biology, University
of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Ramon Crehuet
- Institute
for Advanced Chemistry of Catalonia (IQAC), CSIC, Carrer Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Enrique Marcos
- Protein
Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), CSIC, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Nushin Aghajari
- Molecular
Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, F-69367 Lyon CEDEX 07, France
| | - Martin Willemoës
- The
Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular
Sciences, Department of Biology, University
of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
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13
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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [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: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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14
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Sun S, Chen W, Peng K, Chen X, Chen J. Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20970-20982. [PMID: 38383926 PMCID: PMC10948491 DOI: 10.1007/s11356-024-32362-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.
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Affiliation(s)
- Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Wanqi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kailin Peng
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xueyingzi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Materials, Loughborough University, Loughborough, LE11 3TU, UK.
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15
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Yang J, Li FZ, Arnold FH. Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering. ACS CENTRAL SCIENCE 2024; 10:226-241. [PMID: 38435522 PMCID: PMC10906252 DOI: 10.1021/acscentsci.3c01275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024]
Abstract
Enzymes can be engineered at the level of their amino acid sequences to optimize key properties such as expression, stability, substrate range, and catalytic efficiency-or even to unlock new catalytic activities not found in nature. Because the search space of possible proteins is vast, enzyme engineering usually involves discovering an enzyme starting point that has some level of the desired activity followed by directed evolution to improve its "fitness" for a desired application. Recently, machine learning (ML) has emerged as a powerful tool to complement this empirical process. ML models can contribute to (1) starting point discovery by functional annotation of known protein sequences or generating novel protein sequences with desired functions and (2) navigating protein fitness landscapes for fitness optimization by learning mappings between protein sequences and their associated fitness values. In this Outlook, we explain how ML complements enzyme engineering and discuss its future potential to unlock improved engineering outcomes.
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Affiliation(s)
- Jason Yang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Francesca-Zhoufan Li
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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16
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Gines G, Espada R, Dramé-Maigné A, Baccouche A, Larrouy N, Rondelez Y. Functional analysis of single enzymes combining programmable molecular circuits with droplet-based microfluidics. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01617-1. [PMID: 38409552 DOI: 10.1038/s41565-024-01617-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024]
Abstract
The analysis of proteins at the single-molecule level reveals heterogeneous behaviours that are masked in ensemble-averaged techniques. The digital quantification of enzymes traditionally involves the observation and counting of single molecules partitioned into microcompartments via the conversion of a profluorescent substrate. This strategy, based on linear signal amplification, is limited to a few enzymes with sufficiently high turnover rate. Here we show that combining the sensitivity of an exponential molecular amplifier with the modularity of DNA-enzyme circuits and droplet readout makes it possible to specifically detect, at the single-molecule level, virtually any D(R)NA-related enzymatic activity. This strategy, denoted digital PUMA (Programmable Ultrasensitive Molecular Amplifier), is validated for more than a dozen different enzymes, including many with slow catalytic rate, and down to the extreme limit of apparent single turnover for Streptococcus pyogenes Cas9. Digital counting uniquely yields absolute molar quantification and reveals a large fraction of inactive catalysts in all tested commercial preparations. By monitoring the amplification reaction from single enzyme molecules in real time, we also extract the distribution of activity among the catalyst population, revealing alternative inactivation pathways under various stresses. Our approach dramatically expands the number of enzymes that can benefit from quantification and functional analysis at single-molecule resolution. We anticipate digital PUMA will serve as a versatile framework for accurate enzyme quantification in diagnosis or biotechnological applications. These digital assays may also be utilized to study the origin of protein functional heterogeneity.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France.
| | - Rocίo Espada
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Adèle Dramé-Maigné
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Alexandre Baccouche
- LIMMS, IRL 2820 CNRS-Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Nicolas Larrouy
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
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17
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Willetts A. The Role of Dioxygen in Microbial Bio-Oxygenation: Challenging Biochemistry, Illustrated by a Short History of a Long Misunderstood Enzyme. Microorganisms 2024; 12:389. [PMID: 38399793 PMCID: PMC10891995 DOI: 10.3390/microorganisms12020389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
A Special Issue of Microorganisms devoted to 'Microbial Biocatalysis and Biodegradation' would be incomplete without some form of acknowledgement of the many important roles that dioxygen-dependent enzymes (principally mono- and dioxygenases) play in relevant aspects of bio-oxygenation. This is reflected by the multiple strategic roles that dioxygen -dependent microbial enzymes play both in generating valuable synthons for chemoenzymatic synthesis and in facilitating reactions that help to drive the global geochemical carbon cycle. A useful insight into this can be gained by reviewing the evolution of the current status of 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) from (+)-camphor-grown Pseudomonas putida ATCC 17453, the key enzyme that promotes the initial ring cleavage of this natural bicyclic terpene. Over the last sixty years, the perceived nature of this monooxygenase has transmogrified significantly. Commencing in the 1960s, extensive initial studies consistently reported that the enzyme was a monomeric true flavoprotein dependent on both FMNH2 and nonheme iron as bound cofactors. However, over the last decade, all those criteria have changed absolutely, and the enzyme is currently acknowledged to be a metal ion-independent homodimeric flavin-dependent two-component mono-oxygenase deploying FMNH2 as a cosubstrate. That transition is a paradigm of the ever evolving nature of scientific knowledge.
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Affiliation(s)
- Andrew Willetts
- 4 Sv Ivan, 21400 Sutivan, Croatia;
- Curnow Consultancies, Helston TR13 9PQ, UK
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18
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Chandnani M, Patel D, Patel T, Buch A. Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic Diversity Through Kinetic, Structural and Molecular Docking Analysis. Protein J 2024; 43:96-114. [PMID: 38127181 DOI: 10.1007/s10930-023-10170-0] [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] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Divergently evolved Tartrate dehydrogenase (TDH) exhibits multiple catalytic activities at a single active site; the enzyme from P. putida (pTDH) being structurally and biochemically well-characterized. Occurrence of TDH-associated ability to aerobically metabolize L-tartrate in Bacillus isolates and limited resemblance of ycsA-encoded protein sequences with pTDH rendered Bacillus TDH as an intriguing enzyme with possible catalytic diversity as well as evolutionary significance. The present study explores substrate interactions of TDHs from B. subtilis 168 (168bTDH) and B. licheniformis DSM-13 (429bTDH) through kinetic, structural and molecular docking-based analysis. Heterologously expressed bTDHs, purified from insoluble fractions of E. coli BL21(DE3) cells, could significantly catalyze L-tartrate and meso-tartrate as substrates in forward reaction. Unlike pTDH, bTDHs distinctly and more efficiently catalyzed the reverse reaction using dihydroxyfumarate substrate following sigmoidal kinetics; the ability being ~ 4 fold higher in 168bTDH. Their binding energies predicted from molecular docking, further substantiated the relative substrate specificities, while revealing major residues involved in protein-ligand interactions at active site. The kinetic analysis and homology modelling validated using Ramachandran Plot analysis predicted a dimeric nature for bTDH. Collectively, the results highlight unique catalytic potential of phylogenetically recent bTDHs, offering an important protein engineering target to mediate efficient enantioselective enzymatic biotransformations.
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Affiliation(s)
- Manali Chandnani
- Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Dist. Anand, Changa, Gujarat, 388 421, India
| | - Disha Patel
- Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Dist. Anand, Changa, Gujarat, 388 421, India
| | - Twinkle Patel
- Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Dist. Anand, Changa, Gujarat, 388 421, India
| | - Aditi Buch
- Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Dist. Anand, Changa, Gujarat, 388 421, India.
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19
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Casadevall G, Casadevall J, Duran C, Osuna S. The shortest path method (SPM) webserver for computational enzyme design. Protein Eng Des Sel 2024; 37:gzae005. [PMID: 38431867 DOI: 10.1093/protein/gzae005] [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: 12/22/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | | | - Cristina Duran
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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20
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Song BPC, Ch'ng ACW, Lim TS. Review of phage display: A jack-of-all-trades and master of most biomolecule display. Int J Biol Macromol 2024; 256:128455. [PMID: 38013083 DOI: 10.1016/j.ijbiomac.2023.128455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Phage display was first described by George P. Smith when it was shown that virus particles were capable of presenting foreign proteins on their surface. The technology has paved the way for the evolution of various biomolecules presentation and diverse selection strategies. This unique feature has been applied as a versatile platform for numerous applications in drug discovery, protein engineering, diagnostics, and vaccine development. Over the decades, the limits of biomolecules displayed on phage particles have expanded from peptides to proteomes and even alternative scaffolds. This has allowed phage display to be viewed as a versatile display platform to accommodate various biomolecules ranging from small peptides to larger proteomes which has significantly impacted advancements in the biomedical industry. This review will explore the vast array of biomolecules that have been successfully employed in phage display technology in biomedical research.
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Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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21
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Zhang H, Dierkes RF, Perez-Garcia P, Costanzi E, Dittrich J, Cea PA, Gurschke M, Applegate V, Partus K, Schmeisser C, Pfleger C, Gohlke H, Smits SHJ, Chow J, Streit WR. The metagenome-derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate (PET). FEBS J 2024; 291:70-91. [PMID: 37549040 DOI: 10.1111/febs.16924] [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: 01/31/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Polyethylene terephthalate (PET) is a widely used synthetic polymer and known to contaminate marine and terrestrial ecosystems. Only few PET-active microorganisms and enzymes (PETases) are currently known, and it is debated whether degradation activity for PET originates from promiscuous enzymes with broad substrate spectra that primarily act on natural polymers or other bulky substrates, or whether microorganisms evolved their genetic makeup to accepting PET as a carbon source. Here, we present a predicted diene lactone hydrolase designated PET40, which acts on a broad spectrum of substrates, including PET. It is the first esterase with activity on PET from a GC-rich Gram-positive Amycolatopsis species belonging to the Pseudonocardiaceae (Actinobacteria). It is highly conserved within the genera Amycolatopsis and Streptomyces. PET40 was identified by sequence-based metagenome search using a PETase-specific hidden Markov model. Besides acting on PET, PET40 has a versatile substrate spectrum, hydrolyzing δ-lactones, β-lactam antibiotics, the polyester-polyurethane Impranil® DLN, and various para-nitrophenyl ester substrates. Molecular docking suggests that the PET degradative activity is likely a result of the promiscuity of PET40, as potential binding modes were found for substrates encompassing mono(2-hydroxyethyl) terephthalate, bis(2-hydroxyethyl) terephthalate, and a PET trimer. We also solved the crystal structure of the inactive PET40 variant S178A to 1.60 Å resolution. PET40 is active throughout a wide pH (pH 4-10) and temperature range (4-65 °C) and remarkably stable in the presence of 5% SDS, making it a promising enzyme as a starting point for further investigations and optimization approaches.
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Affiliation(s)
- Hongli Zhang
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Robert F Dierkes
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Germany
| | - Elisa Costanzi
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Pablo A Cea
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marno Gurschke
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Violetta Applegate
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Kristina Partus
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), John von Neumann Institute for Computing and Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
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22
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Feng Y, Lyu X, Cong Y, Miao T, Fang B, Zhang C, Shen Q, Matthews M, Fisher AJ, Zhang JZH, Zhang L, Yang R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction. Int J Biol Macromol 2023; 253:127093. [PMID: 37758108 DOI: 10.1016/j.ijbiomac.2023.127093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Promiscuous enzymes play a crucial role in organism survival and new reaction mining. However, comprehensive mapping of the catalytic and regulatory mechanisms hasn't been well studied due to the characteristic complexity. The cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) with complex epimerization and isomerization was chosen to comprehensively investigate the promiscuous mechanisms. Here, the catalytic frame of ring-opening, cis-enediol mediated catalysis and ring-closing was firstly determined. To map the full view of promiscuous CE, the structure of CsCE complex with the isomerized product glucopyranosyl-β1,4-fructose was determined. Combined with computational calculation, the promiscuity was proved a precise cooperation of the double subsites, loop rearrangement, and intermediate swaying. The flexible loop was like a gear, whose structural reshaping regulates the sway of the intermediates between the two subsites of H377-H188 and H377-H247, and thus regulates the catalytic directions. The different protonated states of cis-enediol intermediate catalyzed by H188 were the key point for the catalysis. The promiscuous enzyme tends to utilize all elements at hand to carry out the promiscuous functions.
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Affiliation(s)
- Yinghui Feng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Tingwei Miao
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Bohuan Fang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuanxi Zhang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Shen
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Melissa Matthews
- Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan; Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
| | - Andrew J Fisher
- Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China; Department of Chemistry, New York University, New York, NY 10003, United States
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
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23
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Tang S, Sun LJ, Pan AQ, Huang J, Wang H, Lin YW. Application of engineered myoglobins for biosynthesis of clofazimine by integration with chemical synthesis. Org Biomol Chem 2023; 21:9603-9609. [PMID: 38014756 DOI: 10.1039/d3ob01687k] [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: 11/29/2023]
Abstract
Significant efforts have been made in the design of artificial metalloenzymes. Myoglobin (Mb), an O2 carrier, has been engineered to exhibit different functions. Herein, we applied a series of engineered Mb mutants with peroxidase activity for biosynthesis of clofazimine (CFZ), a potential drug with a broad-spectrum antiviral activity, by integration with chemical synthesis. Two of those mutants, F43Y Mb and F43Y/T67R Mb, have been shown to efficiently catalyze the oxidative coupling of 2-N-(4-chlorophenyl) benzene-1,2-diamine (N-4-CPBDA) in the presence of H2O2, with 97% yields. The overall catalytic efficiency (kcat/Km) is 46-fold and 82-fold higher than that of WT Mb, respectively. By further combination of this reaction with chemical synthesis, the production of CFZ was accomplished with an isolated yield of 72%. These results showed that engineered Mbs containing the Tyr-heme cross-link (F43Y Mb and F43Y/T67R Mb) exhibit enhanced activity in the oxidative coupling reaction. This study also indicates that the combination of biocatalysis and chemical synthesis avoids the need for the separation of intermediate products, which offers a convenient approach for the total synthesis of the biological compound CFZ.
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Affiliation(s)
- Shuai Tang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Li-Juan Sun
- Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Ai-Qun Pan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Jun Huang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Huamin Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
- Hengyang Medical College, University of South China, Hengyang 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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24
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Capone M, Dell’Orletta G, Nicholls BT, Scholes GD, Hyster TK, Aschi M, Daidone I. Evidence of a Distinctive Enantioselective Binding Mode for the Photoinduced Radical Cyclization of α-Chloroamides in Ene-Reductases. ACS Catal 2023; 13:15310-15321. [PMID: 38058601 PMCID: PMC10696551 DOI: 10.1021/acscatal.3c03934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
We demonstrate here through molecular simulations and mutational studies the origin of the enantioselectivity in the photoinduced radical cyclization of α-chloroacetamides catalyzed by ene-reductases, in particular the Gluconobacter oxidans ene-reductase and the Old Yellow Enzyme 1, which show opposite enantioselectivity. Our results reveal that neither the π-facial selectivity model nor a protein-induced selective stabilization of the transition states is able to explain the enantioselectivity of the radical cyclization in the studied flavoenzymes. We propose a new enantioinduction scenario according to which enantioselectivity is indeed controlled by transition-state stability; however, the relative stability of the prochiral transition states is not determined by direct interaction with the protein but is rather dependent on an inherent degree of freedom within the substrate itself. This intrinsic degree of freedom, distinct from the traditional π-facial exposure mode, can be controlled by the substrate conformational selection upon binding to the enzyme.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
| | - Gianluca Dell’Orletta
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
| | - Bryce T. Nicholls
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Gregory D. Scholes
- Department
of Chemistry, Frick Laboratory, Princeton
University, Princeton, New Jersey 08544, United States
| | - Todd K. Hyster
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Massimiliano Aschi
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
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25
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Porter R, Černoša A, Fernández-Sanmartín P, Cortizas AM, Aranda E, Luo Y, Zalar P, Podlogar M, Gunde-Cimerman N, Gostinčar C. Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae. Microbiol Res 2023; 277:127507. [PMID: 37793281 DOI: 10.1016/j.micres.2023.127507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.
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Affiliation(s)
- Rachel Porter
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anja Černoša
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Paola Fernández-Sanmartín
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Antonio Martínez Cortizas
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Elisabet Aranda
- University of Granada, Institute of Water Research, Environmental Microbiology Group, Ramón y Cajal n4, 18071 Granada, Spain
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 266555, China
| | - Polona Zalar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Matejka Podlogar
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Cene Gostinčar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia.
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26
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Ribeiro AJM, Riziotis IG, Borkakoti N, Thornton JM. Enzyme function and evolution through the lens of bioinformatics. Biochem J 2023; 480:1845-1863. [PMID: 37991346 PMCID: PMC10754289 DOI: 10.1042/bcj20220405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Enzymes have been shaped by evolution over billions of years to catalyse the chemical reactions that support life on earth. Dispersed in the literature, or organised in online databases, knowledge about enzymes can be structured in distinct dimensions, either related to their quality as biological macromolecules, such as their sequence and structure, or related to their chemical functions, such as the catalytic site, kinetics, mechanism, and overall reaction. The evolution of enzymes can only be understood when each of these dimensions is considered. In addition, many of the properties of enzymes only make sense in the light of evolution. We start this review by outlining the main paradigms of enzyme evolution, including gene duplication and divergence, convergent evolution, and evolution by recombination of domains. In the second part, we overview the current collective knowledge about enzymes, as organised by different types of data and collected in several databases. We also highlight some increasingly powerful computational tools that can be used to close gaps in understanding, in particular for types of data that require laborious experimental protocols. We believe that recent advances in protein structure prediction will be a powerful catalyst for the prediction of binding, mechanism, and ultimately, chemical reactions. A comprehensive mapping of enzyme function and evolution may be attainable in the near future.
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Affiliation(s)
- Antonio J. M. Ribeiro
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Ioannis G. Riziotis
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Neera Borkakoti
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Janet M. Thornton
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
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27
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Reja A, Pal S, Mahato K, Saha B, Delle Piane M, Pavan GM, Das D. Emergence of Photomodulated Protometabolism by Short Peptide-Based Assemblies. J Am Chem Soc 2023; 145:21114-21121. [PMID: 37708200 DOI: 10.1021/jacs.3c08158] [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: 09/16/2023]
Abstract
In the early Earth, rudimentary enzymes must have utilized the available light energy source to modulate protometabolic processes. Herein, we report the light-responsive C-C bond manipulation via short peptide-based assemblies bound to the photosensitive molecular cofactor (azo-based photoswitch) where the energy of the light source regulated the binding sites which subsequently modulated the retro-aldolase activity. In the presence of a continual source of high-energy photons, temporal realization of a catalytically more proficient state could be achieved under nonequilibrium conditions. Further, the hydrophobic surface of peptide assemblies facilitated the binding of an orthogonal molecular catalyst that showed augmented activity (promiscuous hydrolytic activity) upon binding. This latent activity was utilized for the in situ generation of light-sensitive cofactor that subsequently modulated the retro-aldolase activity, thus creating a reaction network.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Sumit Pal
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Kishalay Mahato
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Baishakhi Saha
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Massimo Delle Piane
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Dibyendu Das
- Department of Chemical Sciences and CAFM, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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28
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Perez-Garcia P, Chow J, Costanzi E, Gurschke M, Dittrich J, Dierkes RF, Molitor R, Applegate V, Feuerriegel G, Tete P, Danso D, Thies S, Schumacher J, Pfleger C, Jaeger KE, Gohlke H, Smits SHJ, Schmitz RA, Streit WR. An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate. Commun Chem 2023; 6:193. [PMID: 37697032 PMCID: PMC10495362 DOI: 10.1038/s42004-023-00998-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 Å. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Elisa Costanzi
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marno Gurschke
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robert F Dierkes
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Violetta Applegate
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Prince Tete
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Dominik Danso
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Julia Schumacher
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
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29
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da Silva JD, Bens L, Santos AJDC, Lavigne R, Soares J, Melo LDR, Vallino M, Dias RS, Drulis-Kawa Z, de Paula SO, Wagemans J. Isolation and Characterization of the Acadevirus Members BigMira and MidiMira Infecting a Highly Pathogenic Proteus mirabilis Strain. Microorganisms 2023; 11:2141. [PMID: 37763984 PMCID: PMC10537623 DOI: 10.3390/microorganisms11092141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
Proteus mirabilis is an opportunistic pathogen and is responsible for more than 40% of all cases of catheter-associated urinary tract infections (CAUTIs). Healthcare-associated infections have been aggravated by the constant emergence of antibiotic-resistant bacterial strains. Because of this, the use of phages to combat bacterial infections gained renewed interest. In this study, we describe the biological and genomic features of two P. mirabilis phages, named BigMira and MidiMira. These phages belong to the Acadevirus genus (family Autographiviridae). BigMira and MidiMira are highly similar, differing only in four missense mutations in their phage tail fiber. These mutations are sufficient to impact the phages' depolymerase activity. Subsequently, the comparative genomic analysis of ten clinical P. mirabilis strains revealed differences in their antibiotic resistance profiles and lipopolysaccharide locus, with the latter potentially explaining the host range data of the phages. The massive presence of antimicrobial resistance genes, especially in the phages' isolation strain P. mirabilis MCS, highlights the challenges in treating infections caused by multidrug-resistant bacteria. The findings reinforce BigMira and MidiMira phages as candidates for phage therapy purposes.
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Affiliation(s)
- Jéssica Duarte da Silva
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Lene Bens
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
| | - Adriele J. do Carmo Santos
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
| | - José Soares
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Luís D. R. Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy;
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil;
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, 50-335 Wroclaw, Poland;
| | - Sérgio Oliveira de Paula
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil;
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
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30
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Wang C, Liu C, Zhu X, Peng Q, Ma Q. Catalytic site flexibility facilitates the substrate and catalytic promiscuity of Vibrio dual lipase/transferase. Nat Commun 2023; 14:4795. [PMID: 37558668 PMCID: PMC10412561 DOI: 10.1038/s41467-023-40455-y] [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: 01/26/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Although enzyme catalysis is typified by high specificity, enzymes can catalyze various substrates (substrate promiscuity) and/or different reaction types (catalytic promiscuity) using a single active site. This interesting phenomenon is widely distributed in enzyme catalysis, with both fundamental and applied importance. To date, the mechanistic understanding of enzyme promiscuity is very limited. Herein, we report the structural mechanism underlying the substrate and catalytic promiscuity of Vibrio dual lipase/transferase (VDLT). Crystal structures of the VDLT from Vibrio alginolyticus (ValDLT) and its fatty acid complexes were solved, revealing prominent structural flexibility. In particular, the "Ser-His-Asp" catalytic triad machinery of ValDLT contains an intrinsically flexible oxyanion hole. Analysis of ligand-bound structures and mutagenesis showed that the flexible oxyanion hole and other binding residues can undergo distinct conformational changes to facilitate substrate and catalytic promiscuity. Our study reveals a previously unknown flexible form of the famous catalytic triad machinery and proposes a "catalytic site tuning" mechanism to expand the mechanistic paradigm of enzyme promiscuity.
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Affiliation(s)
- Chongyang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changshui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaochuan Zhu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Quancai Peng
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Qingjun Ma
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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31
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Fu W, Neris NM, Fu Y, Zhao Y, Krohn-Hansen B, Liu P, Yang Y. Enzyme-controlled stereoselective radical cyclization to arenes enabled by metalloredox biocatalysis. Nat Catal 2023; 6:628-636. [PMID: 38404758 PMCID: PMC10882986 DOI: 10.1038/s41929-023-00986-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 06/13/2023] [Indexed: 02/27/2024]
Abstract
The effective induction of high levels of stereocontrol for free radical-mediated transformations represents a notorious challenge in asymmetric catalysis. Herein, we describe a novel metalloredox biocatalysis strategy to repurpose natural cytochromes P450 to catalyse asymmetric radical cyclisation to arenes through an unnatural electron transfer mechanism. Empowered by directed evolution, engineered P450s allowed diverse radical cyclisation selectivities to be accomplished in a catalyst-controlled fashion: P450arc1 and P450arc2 facilitated enantioconvergent transformations of racemic substrates, giving rise to either enantiomer of the product with excellent total turnover numbers (up to 12,000). In addition to these enantioconvergent variants, another engineered radical cyclase, P450arc3, permitted efficient kinetic resolution of racemic chloride substrates (S factor = 18). Furthermore, computational studies revealed a proton-coupled electron transfer (PCET) mechanism for the radical-polar crossover step, suggesting the potential role of the haem carboxylate as a base catalyst. Collectively, the excellent tunability of this metalloenzyme family provides an exciting platform for harnessing free radical intermediates for asymmetric catalysis.
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Affiliation(s)
- Wenzhen Fu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Natalia M. Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Yue Fu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yunlong Zhao
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Benjamin Krohn-Hansen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, USA
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32
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Leone L, Muñoz-García AB, D'Alonzo D, Pavone V, Nastri F, Lombardi A. Peptide-based metalloporphyrin catalysts: unveiling the role of the metal ion in indole oxidation. J Inorg Biochem 2023; 246:112298. [PMID: 37379767 DOI: 10.1016/j.jinorgbio.2023.112298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
Over the last decades, much effort has been devoted to the construction of protein and peptide-based metalloporphyrin catalysts capable of promoting difficult transformations with high selectivity. In this context, mechanistic studies are fundamental to elucidate all the factors that contribute to catalytic performances and product selectivity. In our previous work, we selected the synthetic peptide-porphyrin conjugate MnMC6*a as a proficient catalyst for indole oxidation, promoting the formation of a 3-oxindole derivative with unprecedented selectivity. In this work, we have evaluated the role of the metal ion in affecting reaction outcome, by replacing manganese with iron in the MC6*a scaffold. Even though product selectivity is not altered upon metal substitution, FeMC6*a shows a lower substrate conversion and prolonged reaction times with respect to its manganese analogue. Experimental and theoretical studies have enabled us to delineate the reaction free energy profiles for both catalysts, indicating different thermodynamic limiting steps, depending on the nature of the metal ion.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Ana Belén Muñoz-García
- Department of Physics "Ettore Pancini", University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy.
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy.
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Murray J, Hodgson DRW, O’Donoghue AC. Going Full Circle with Organocatalysis and Biocatalysis: The Latent Potential of Cofactor Mimics in Asymmetric Synthesis. J Org Chem 2023; 88:7619-7629. [PMID: 37126859 PMCID: PMC10278144 DOI: 10.1021/acs.joc.2c02747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 05/03/2023]
Abstract
Many enzymes work in tandem with small molecule cofactors, which have inspired organocatalyst designs. Chemical modification of cofactor scaffolds has increased organocatalytic reactivity and reaction scope. This synopsis presents a selection of recent advances in the use of cofactors (native and mimics) in organocatalysis and biocatalysis. We aim to highlight the benefits of combining fundamental knowledge gained in both bio- and organo-catalysis for asymmetric biocatalysis.
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Affiliation(s)
- Jacob Murray
- Department of Chemistry, Durham University, South Road, Durham DH1
3LE, United
Kingdom
| | - David R. W. Hodgson
- Department of Chemistry, Durham University, South Road, Durham DH1
3LE, United
Kingdom
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34
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Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabrière E, Daudé D, Elias MH. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541809. [PMID: 37292757 PMCID: PMC10245850 DOI: 10.1101/2023.05.22.541809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver for the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of the lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being > 1,000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, ~1,000,000-fold and beyond, since some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops, as revealed by a suite of crystal structures. This suggests that specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining an enzyme activity profile.
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Affiliation(s)
- Pauline Jacquet
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Raphaël Billot
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Amir Shimon
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Nathan Hoekstra
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Céline Bergonzi
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Anthony Jenks
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Eric Chabrière
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - David Daudé
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Mikael H. Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
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Deng J, Cui Q. Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA. J Am Chem Soc 2023; 145:11333-11347. [PMID: 37172218 PMCID: PMC10810092 DOI: 10.1021/jacs.3c02423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Residues beyond the first coordination shell are often observed to make considerable cumulative contributions in enzymes. Due to typically indirect perturbations of multiple physicochemical properties of the active site, however, their individual and specific roles in enzyme catalysis and disease-causing mutations remain difficult to predict and understand at the molecular level. Here we analyze the contributions of several second-shell residues in phosphate-irrepressible alkaline phosphatase of flavobacterium (PafA), a representative system as one of the most efficient enzymes. By adopting a multifaceted approach that integrates quantum-mechanical/molecular-mechanical free energy computations, molecular-mechanical molecular dynamics simulations, and density functional theory cluster model calculations, we probe the rate-limiting phosphoryl transfer step and structural properties of all relevant enzyme states. In combination with available experimental data, our computational results show that mutations of the studied second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and therefore substrate binding, while they do not affect the ground state or alter the nature of phosphoryl transfer transition state significantly. Several second-shell mutations also modulate the active site hydration level, which in turn influences the energetics of phosphoryl transfer. These mechanistic insights also help inform strategies that may improve the efficiency of enzyme design and engineering by going beyond the current focus on the first coordination shell.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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36
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Fu Y, Liu X, Xia Y, Guo X, Guo J, Zhang J, Zhao W, Wu Y, Wang J, Zhong F. Whole-cell-catalyzed hydrogenation/deuteration of aryl halides with a genetically repurposed photodehalogenase. Chem 2023. [DOI: 10.1016/j.chempr.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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37
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Hanreich S, Bonandi E, Drienovská I. Design of Artificial Enzymes: Insights into Protein Scaffolds. Chembiochem 2023; 24:e202200566. [PMID: 36418221 DOI: 10.1002/cbic.202200566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.
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Affiliation(s)
- Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Elisa Bonandi
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
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38
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Kato S, Onoda A, Schwaneberg U, Hayashi T. Evolutionary Engineering of a Cp*Rh(III) Complex-Linked Artificial Metalloenzyme with a Chimeric β-Barrel Protein Scaffold. J Am Chem Soc 2023; 145. [PMID: 36892401 PMCID: PMC10119979 DOI: 10.1021/jacs.3c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 03/10/2023]
Abstract
Evolutionary engineering of our previously reported Cp*Rh(III)-linked artificial metalloenzyme was performed based on a DNA recombination strategy to improve its catalytic activity toward C(sp2)-H bond functionalization. Improved scaffold design was achieved with α-helical cap domains of fatty acid binding protein (FABP) embedded within the β-barrel structure of nitrobindin (NB) as a chimeric protein scaffold for the artificial metalloenzyme. After optimization of the amino acid sequence by directed evolution methodology, an engineered variant, designated NBHLH1(Y119A/G149P) with enhanced performance and enhanced stability was obtained. Additional rounds of metalloenzyme evolution provided a Cp*Rh(III)-linked NBHLH1(Y119A/G149P) variant with a >35-fold increase in catalytic efficiency (kcat/KM) for cycloaddition of oxime and alkyne. Kinetic studies and MD simulations revealed that aromatic amino acid residues in the confined active-site form a hydrophobic core which binds to aromatic substrates adjacent to the Cp*Rh(III) complex. The metalloenzyme engineering process based on this DNA recombination strategy will serve as a powerful method for extensive optimization of the active-sites of artificial metalloenzymes.
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Affiliation(s)
- Shunsuke Kato
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Akira Onoda
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute
of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Takashi Hayashi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
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Guo H, Sun N, Guo J, Zhou TP, Tang L, Zhang W, Deng Y, Liao RZ, Wu Y, Wu G, Zhong F. Expanding the Promiscuity of a Copper-Dependent Oxidase for Enantioselective Cross-Coupling of Indoles. Angew Chem Int Ed Engl 2023; 62:e202219034. [PMID: 36789864 DOI: 10.1002/anie.202219034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/16/2023]
Abstract
Herein, we disclose the highly enantioselective oxidative cross-coupling of 3-hydroxyindole esters with various nucleophilic partners as catalyzed by copper efflux oxidase. The biocatalytic transformation delivers functionalized 2,2-disubstituted indolin-3-ones with excellent optical purity (90-99 % ee), which exhibited anticancer activity against MCF-7 cell lines, as shown by preliminary biological evaluation. Mechanistic studies and molecular docking results suggest the formation of a phenoxyl radical and enantiocontrol facilitated by a suited enzyme chiral pocket. This study is significant with regard to expanding the catalytic repertoire of natural multicopper oxidases as well as enlarging the synthetic toolbox for sustainable asymmetric oxidative coupling.
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Affiliation(s)
- Huan Guo
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Ningning Sun
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Juan Guo
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Tai-Ping Zhou
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Langyu Tang
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Wentao Zhang
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Yaming Deng
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Rong-Zhen Liao
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Yuzhou Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Guojiao Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
| | - Fangrui Zhong
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Luoyu Road 1037, Wuhan, 430074, China
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40
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Yu Y, Li F, Li J, Zheng X, Tian H, Mahmut Z, Du Y, Dai Y, Wang L. Lipase-catalyzed hydrazine insertion for the synthesis of N'-alkyl benzohydrazides. Biotechnol Appl Biochem 2023; 70:130-136. [PMID: 35285069 DOI: 10.1002/bab.2335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/22/2022] [Indexed: 11/07/2022]
Abstract
N'-alkyl benzohydrazides are classic organic compounds that have been widely utilized in organic chemistry. In this study, an efficient method was developed for the synthesis of N'-alkyl benzohydrazides by hydrazine insertion catalyzed by lipase. Under the optimal conditions (Morita-Baylis-Hillman ketone [1 mmol], phenylhydrazine [1.3 mmol], N,N-dimethylformamide [2 ml], lipase [20 mg], room temperature, 12 h), satisfactory yields (71-97%) and substrate tolerance were obtained when porcine pancreatic lipase was used as biocatalyst. These findings imply the great potential for the lipase-catalyzed synthesis of N'-alkyl benzohydrazides and extend the utilization of lipase in organic chemistry.
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Affiliation(s)
- Yue Yu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Fengxi Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Jiapeng Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Xin Zheng
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Haochen Tian
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Zulpiya Mahmut
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Yanan Du
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Yuyin Dai
- Department of Nuclear Medicine, the First Hospital of Jilin University, Changchun, China
| | - Lei Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
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41
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Holt BA, Lim HS, Sivakumar A, Phuengkham H, Su M, Tuttle M, Xu Y, Liakakos H, Qiu P, Kwong GA. Embracing enzyme promiscuity with activity-based compressed biosensing. CELL REPORTS METHODS 2023; 3:100372. [PMID: 36814844 PMCID: PMC9939361 DOI: 10.1016/j.crmeth.2022.100372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]
Abstract
The development of protease-activatable drugs and diagnostics requires identifying substrates specific to individual proteases. However, this process becomes increasingly difficult as the number of target proteases increases because most substrates are promiscuously cleaved by multiple proteases. We introduce a method-substrate libraries for compressed sensing of enzymes (SLICE)-for selecting libraries of promiscuous substrates that classify protease mixtures (1) without deconvolution of compressed signals and (2) without highly specific substrates. SLICE ranks substrate libraries using a compression score (C), which quantifies substrate orthogonality and protease coverage. This metric is predictive of classification accuracy across 140 in silico (Pearson r = 0.71) and 55 in vitro libraries (r = 0.55). Using SLICE, we select a two-substrate library to classify 28 samples containing 11 enzymes in plasma (area under the receiver operating characteristic curve [AUROC] = 0.93). We envision that SLICE will enable the selection of libraries that capture information from hundreds of enzymes using fewer substrates for applications like activity-based sensors for imaging and diagnostics.
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Affiliation(s)
- Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hong Seo Lim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Anirudh Sivakumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hathaichanok Phuengkham
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Melanie Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - McKenzie Tuttle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Yilin Xu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Haley Liakakos
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Gabriel A. Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA 30332, USA
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA 30332, USA
- Integrated Cancer Research Center, Georgia Tech, Atlanta, GA 30332, USA
- Georgia ImmunoEngineering Consortium, Georgia Tech and Emory University, Atlanta, GA 30332, USA
- Emory School of Medicine, Atlanta, GA 30332, USA
- Emory Winship Cancer Institute, Atlanta, GA 30322, USA
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42
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Sun LJ, Yuan H, Xu JK, Luo J, Lang JJ, Wen GB, Tan X, Lin YW. Phenoxazinone Synthase-like Activity of Rationally Designed Heme Enzymes Based on Myoglobin. Biochemistry 2023; 62:369-377. [PMID: 34665595 DOI: 10.1021/acs.biochem.1c00554] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The design of functional metalloenzymes is attractive for the biosynthesis of biologically important compounds, such as phenoxazinones and phenazines catalyzed by native phenoxazinone synthase (PHS). To design functional heme enzymes, we used myoglobin (Mb) as a model protein and introduced an artificial CXXC motif into the heme distal pocket by F46C and L49C mutations, which forms a de novo disulfide bond, as confirmed by the X-ray crystal structure. We further introduced a catalytic Tyr43 into the heme distal pocket and found that the F43Y/F46C/L49C Mb triple mutant and the previously designed F43Y/F46S Mb exhibit PHS-like activity (80-98% yields in 5-15 min), with the catalytic efficiency exceeding those of natural metalloenzymes, including o-aminophenol oxidase, laccase, and dye-decolorizing peroxidase. Moreover, we showed that the oxidative coupling product of 1,6-disulfonic-2,7-diaminophenazine is a potential pH indicator, with the orange-magenta color change at pH 4-5 (pKa = 4.40). Therefore, this study indicates that functional heme enzymes can be rationally designed by structural modifications of Mb, exhibiting the functionality of the native PHS for green biosynthesis.
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Affiliation(s)
- Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jie Luo
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Jia-Jia Lang
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- Hengyang Medical School, University of South China, Hengyang 421001, China.,Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
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Babić M, Janković P, Marchesan S, Mauša G, Kalafatovic D. Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs. J Chem Inf Model 2022; 62:6398-6410. [PMID: 36223497 DOI: 10.1021/acs.jcim.2c00977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ester hydrolysis is of wide biomedical interest, spanning from the green synthesis of pharmaceuticals to biomaterials' development. Existing peptide-based catalysts exhibit low catalytic efficiency compared to natural enzymes, due to the conformational heterogeneity of peptides. Moreover, there is lack of understanding of the correlation between the primary sequence and catalytic function. For this purpose, we statistically analyzed 22 EC 3.1 hydrolases with known catalytic triads, characterized by unique and well-defined mechanisms. The aim was to identify patterns at the sequence level that will better inform the creation of short peptides containing important information for catalysis, based on the catalytic triad, oxyanion holes and the triad residues microenvironments. Moreover, fragmentation schemes of the primary sequence of selected enzymes alongside the study of their amino acid frequencies, composition, and physicochemical properties are proposed. The results showed highly conserved catalytic sites with distinct positional patterns and chemical microenvironments that favor catalysis and revealed variations in catalytic site composition that could be useful for the design of minimalistic catalysts.
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Affiliation(s)
- Marko Babić
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Patrizia Janković
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127Trieste, Italy
| | - Goran Mauša
- Faculty of Engineering, University of Rijeka, 51000Rijeka, Croatia
| | - Daniela Kalafatovic
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia.,Center for Advanced Computing and Modeling, University of Rijeka, 51000Rijeka, Croatia
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Transient Glycolytic Complexation of Arsenate Enhances Resistance in the Enteropathogen Vibrio cholerae. mBio 2022; 13:e0165422. [PMID: 36102515 PMCID: PMC9601151 DOI: 10.1128/mbio.01654-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous presence of toxic arsenate (AsV) in the environment has raised mechanisms of resistance in all living organisms. Generally, bacterial detoxification of AsV relies on its reduction to arsenite (AsIII) by ArsC, followed by the export of AsIII by ArsB. However, how pathogenic species resist this metalloid remains largely unknown. Here, we found that Vibrio cholerae, the etiologic agent of the diarrheal disease cholera, outcompetes other enteropathogens when grown on millimolar concentrations of AsV. To do so, V. cholerae uses, instead of ArsCB, the AsV-inducible vc1068-1071 operon (renamed var for vibrio arsenate resistance), which encodes the arsenate repressor ArsR, an alternative glyceraldehyde-3-phosphate dehydrogenase, a putative phosphatase, and the AsV transporter ArsJ. In addition to Var, V. cholerae induces oxidative stress-related systems to counter reactive oxygen species (ROS) production caused by intracellular AsV. Characterization of the var mutants suggested that these proteins function independently from one another and play critical roles in preventing deleterious effects on the cell membrane potential and growth derived from the accumulation AsV. Mechanistically, we demonstrate that V. cholerae complexes AsV with the glycolytic intermediate 3-phosphoglycerate into 1-arseno-3-phosphoglycerate (1As3PG). We further show that 1As3PG is not transported outside the cell; instead, it is subsequently dissociated to enable extrusion of free AsV through ArsJ. Collectively, we propose the formation of 1As3PG as a transient metabolic storage of AsV to curb the noxious effect of free AsV. This study advances our understanding of AsV resistance in bacteria and underscores new points of vulnerability that might be an attractive target for antimicrobial interventions. IMPORTANCE Even though resistance to arsenate has been extensively investigated in environmental bacteria, how enteric pathogens tolerate this toxic compound remains unknown. Here, we found that the cholera pathogen V. cholerae exhibits increased resistance to arsenate compared to closely related enteric pathogens. Such resistance is promoted not by ArsC-dependent reduction of arsenate to arsenite but by an operon encoding an arsenate transporter (ArsJ), an alternative glyceraldehyde 3-phosphate dehydrogenase (VarG), and a putative, uncharacterized phosphatase (VarH). Mechanistically, we demonstrate that V. cholerae detoxifies arsenate by complexing it with the glycolytic intermediate 3-phosphoglycerate into 1-arseno-3-phosphoglycerate (1As3PG). 1As3PG is not transported outside the cell; instead, it is subsequently dissociated by VarH to enable extrusion of free arsenate through ArsJ. Collectively, this study proposes a novel mechanism for arsenate detoxification, entirely independent of arsenate reduction and arsenite extrusion, that enhances V. cholerae resistance to this metalloid compared to other enteric pathogens.
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Blazeck J, Karamitros CS, Ford K, Somody C, Qerqez A, Murray K, Burkholder NT, Marshall N, Sivakumar A, Lu WC, Tan B, Lamb C, Tanno Y, Siddiqui MY, Ashoura N, Coma S, Zhang XM, McGovern K, Kumada Y, Zhang YJ, Manfredi M, Johnson KA, D’Arcy S, Stone E, Georgiou G. Bypassing evolutionary dead ends and switching the rate-limiting step of a human immunotherapeutic enzyme. Nat Catal 2022; 5:952-967. [PMID: 36465553 PMCID: PMC9717613 DOI: 10.1038/s41929-022-00856-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
The Trp metabolite kynurenine (KYN) accumulates in numerous solid tumours and mediates potent immunosuppression. Bacterial kynureninases (KYNases), which preferentially degrade kynurenine, can relieve immunosuppression in multiple cancer models, but immunogenicity concerns preclude their clinical use, while the human enzyme (HsKYNase) has very low activity for kynurenine and shows no therapeutic effect. Using fitness selections, we evolved a HsKYNase variant with 27-fold higher activity, beyond which exploration of >30 evolutionary trajectories involving the interrogation of >109 variants led to no further improvements. Introduction of two amino acid substitutions conserved in bacterial KYNases reduced enzyme fitness but potentiated rapid evolution of variants with ~500-fold improved activity and reversed substrate specificity, resulting in an enzyme capable of mediating strong anti-tumour effects in mice. Pre-steady-state kinetics revealed a switch in rate-determining step attributable to changes in both enzyme structure and conformational dynamics. Apart from its clinical significance, our work highlights how rationally designed substitutions can potentiate trajectories that overcome barriers in protein evolution.
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Affiliation(s)
- John Blazeck
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Christos S. Karamitros
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Ford
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Catrina Somody
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Ahlam Qerqez
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Nathaniel T. Burkholder
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Nicholas Marshall
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Anirudh Sivakumar
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Wei-Cheng Lu
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Bing Tan
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Menna Y. Siddiqui
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Norah Ashoura
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Silvia Coma
- Ikena Oncology, Cambridge, Massachusetts, USA
| | | | | | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
| | | | - Kenneth A. Johnson
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Sheena D’Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Everett Stone
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA
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46
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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47
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Chow J, Perez‐Garcia P, Dierkes R, Streit WR. Microbial enzymes will offer limited solutions to the global plastic pollution crisis. Microb Biotechnol 2022; 16:195-217. [PMID: 36099200 PMCID: PMC9871534 DOI: 10.1111/1751-7915.14135] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/09/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
Global economies depend on the use of fossil-fuel-based polymers with 360-400 million metric tons of synthetic polymers being produced per year. Unfortunately, an estimated 60% of the global production is disposed into the environment. Within this framework, microbiologists have tried to identify plastic-active enzymes over the past decade. Until now, this research has largely failed to deliver functional biocatalysts acting on the commodity polymers such as polyethylene (PE), polypropylene (PP), polyvinylchloride (PVC), ether-based polyurethane (PUR), polyamide (PA), polystyrene (PS) and synthetic rubber (SR). However, few enzymes are known to act on low-density and low-crystalline (amorphous) polyethylene terephthalate (PET) and ester-based PUR. These above-mentioned polymers represent >95% of all synthetic plastics produced. Therefore, the main challenge microbiologists are currently facing is in finding polymer-active enzymes targeting the majority of fossil-fuel-based plastics. However, identifying plastic-active enzymes either to implement them in biotechnological processes or to understand their potential role in nature is an emerging research field. The application of these enzymes is still in its infancy. Here, we summarize the current knowledge on microbial plastic-active enzymes, their global distribution and potential impact on plastic degradation in industrial processes and nature. We further outline major challenges in finding novel plastic-active enzymes, optimizing known ones by synthetic approaches and problems arising through falsely annotated and unfiltered use of database entries. Finally, we highlight potential biotechnological applications and possible re- and upcycling concepts using microorganisms.
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Affiliation(s)
- Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Robert Dierkes
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
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48
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Ye DY, Noh MH, Moon JH, Milito A, Kim M, Lee JW, Yang JS, Jung GY. Kinetic compartmentalization by unnatural reaction for itaconate production. Nat Commun 2022; 13:5353. [PMID: 36097012 PMCID: PMC9468356 DOI: 10.1038/s41467-022-33033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Physical compartmentalization of metabolism using membranous organelles in eukaryotes is helpful for chemical biosynthesis to ensure the availability of substrates from competitive metabolic reactions. Bacterial hosts lack such a membranous system, which is one of the major limitations for efficient metabolic engineering. Here, we employ kinetic compartmentalization with the introduction of an unnatural enzymatic reaction by an engineered enzyme as an alternative strategy to enable substrate availability from competitive reactions through kinetic isolation of metabolic pathways. As a proof of concept, we kinetically isolate the itaconate synthetic pathway from the tricarboxylic acid cycle in Escherichia coli, which is natively separated by mitochondrial membranes in Aspergillus terreus. Specifically, 2-methylcitrate dehydratase is engineered to alternatively catalyze citrate and kinetically secure cis-aconitate for efficient production using a high-throughput screening system. Itaconate production can be significantly improved with kinetic compartmentalization and its strategy has the potential to be widely applicable.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea. .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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49
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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50
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Zhang S, Li Y, Sun S, Liu L, Mu X, Liu S, Jiao M, Chen X, Chen K, Ma H, Li T, Liu X, Wang H, Zhang J, Yang J, Zhang XD. Single-atom nanozymes catalytically surpassing naturally occurring enzymes as sustained stitching for brain trauma. Nat Commun 2022; 13:4744. [PMID: 35961961 PMCID: PMC9374753 DOI: 10.1038/s41467-022-32411-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/29/2022] [Indexed: 01/10/2023] Open
Abstract
Regenerable nanozymes with high catalytic stability and sustainability are promising substitutes for naturally-occurring enzymes but are limited by insufficient and non-selective catalytic activities. Herein, we developed single-atom nanozymes of RhN4, VN4, and Fe-Cu-N6 with catalytic activities surpassing natural enzymes. Notably, Rh/VN4 preferably forms an Rh/V-O-N4 active center to decrease reaction energy barriers and mediates a “two-sided oxygen-linked” reaction path, showing 4 and 5-fold higher affinities in peroxidase-like activity than the FeN4 and natural horseradish peroxidase. Furthermore, RhN4 presents a 20-fold improved affinity in the catalase-like activity compared to the natural catalase; Fe-Cu-N6 displays selectivity towards the superoxide dismutase-like activity; VN4 favors a 7-fold higher glutathione peroxidase-like activity than the natural glutathione peroxidase. Bioactive sutures with Rh/VN4 show recyclable catalytic features without apparent decay in 1 month and accelerate the scalp healing from brain trauma by promoting the vascular endothelial growth factor, regulating the immune cells like macrophages, and diminishing inflammation. The catalytic activity of regenerable nanozymes is currently the bottle neck for their wider employment. Here, the authors report on single-atom nanozymes of RhN4, VN4, and Fe-Cu-N6 with higher catalytic activities than natural enzymes, and demonstrate the Rh/VN4 recyclability and scalp healing properties in bioactive sutures.
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Affiliation(s)
- Shaofang Zhang
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China
| | - Yonghui Li
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China
| | - Si Sun
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China
| | - Ling Liu
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Xiaoyu Mu
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Shuhu Liu
- Beijing Synchrotron Radiation Facility (BSRF), Institute of High Energy Physics (IHEP), Chinese Academy of Sciences (CAS), Beijing, 100049, China
| | - Menglu Jiao
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China
| | - Xinzhu Chen
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Ke Chen
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Huizhen Ma
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China
| | - Tuo Li
- Department of Neurosurgery and Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xiaoyu Liu
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China
| | - Hao Wang
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Jianning Zhang
- Department of Neurosurgery and Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Jiang Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xiao-Dong Zhang
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin, 300350, China. .,Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China.
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