1
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Miller AH, Martins IBS, Blagova EV, Wilson KS, Duhme-Klair AK. Kinetic and structural analysis of redox-reversible artificial imine reductases. J Inorg Biochem 2024; 260:112691. [PMID: 39126757 DOI: 10.1016/j.jinorgbio.2024.112691] [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: 06/10/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Three artificial imine reductases, constructed via supramolecular anchoring utilising FeIII-azotochelin, a natural siderophore, to bind an iridium-containing catalyst to periplasmic siderophore-binding protein (PBP) scaffolds, have previously been synthesised and subjected to catalytic testing. Despite exhibiting high homology and possessing conserved siderophore anchor coordinating residues, the three artificial metalloenzymes (ArMs) displayed significant variability in turnover frequencies (TOFs). To further understand the catalytic properties of these ArMs, their kinetic behaviour was evaluated with respect to the reduction of three cyclic imines: dihydroisoquinoline, harmaline, and papaverine. Kinetic analyses revealed that all examined ArMs adhere to Michaelis-Menten kinetics, with the most pronounced saturation profile observed for the substrate harmaline. Additionally, molecular docking studies suggested varied hydrogen-bonding interactions between substrates and residues within the artificial binding pocket. Pi-stacking and pi-cation interactions were identified for harmaline and papaverine, corroborating the higher affinity of these substrates for the ArMs in comparison to dihydroisoquinoline. Furthermore, it was demonstrated that multiple cavities are capable of accommodating substrates in close proximity to the catalytic centre, thereby rationalising the moderate enantioselectivity conferred by the unmodified scaffolds.
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Affiliation(s)
- Alex H Miller
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Ingrid B S Martins
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Elena V Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Keith S Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Anne-K Duhme-Klair
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom.
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2
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Xu Y, Li F, Xie H, Liu Y, Han W, Wu J, Cheng L, Wang C, Li Z, Wang L. Directed evolution of Escherichia coli surface-displayed Vitreoscilla hemoglobin as an artificial metalloenzyme for the synthesis of 5-imino-1,2,4-thiadiazoles. Chem Sci 2024; 15:7742-7748. [PMID: 38784746 PMCID: PMC11110144 DOI: 10.1039/d4sc00005f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Artificial metalloenzymes (ArMs) are constructed by anchoring organometallic catalysts to an evolvable protein scaffold. They present the advantages of both components and exhibit considerable potential for the in vivo catalysis of new-to-nature reactions. Herein, Escherichia coli surface-displayed Vitreoscilla hemoglobin (VHbSD-Co) that anchored the cobalt porphyrin cofactor instead of the original heme cofactor was used as an artificial thiourea oxidase (ATOase) to synthesize 5-imino-1,2,4-thiadiazoles. After two rounds of directed evolution using combinatorial active-site saturation test/iterative saturation mutagenesis (CAST/ISM) strategy, the evolved six-site mutation VHbSD-Co (6SM-VHbSD-Co) exhibited significant improvement in catalytic activity, with a broad substrate scope (31 examples) and high yields with whole cells. This study shows the potential of using VHb ArMs in new-to-nature reactions and demonstrates the applicability of E. coli surface-displayed methods to enhance catalytic properties through the substitution of porphyrin cofactors in hemoproteins in vivo.
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Affiliation(s)
- Yaning Xu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Fengxi Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Hanqing Xie
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Yuyang Liu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Weiwei Han
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Junhao Wu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Lei Cheng
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University Changchun 130023 P. R. China
| | - Zhengqiang Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
| | - Lei Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University Changchun 130023 P. R. China
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3
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Tiwari OS, Gazit E. Characterization of amyloid-like metal-amino acid assemblies with remarkable catalytic activity. Methods Enzymol 2024; 697:181-209. [PMID: 38816123 DOI: 10.1016/bs.mie.2024.01.018] [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] [Indexed: 06/01/2024]
Abstract
While enzymes are potentially useful in various applications, their limited operational stability and production costs have led to an extensive search for stable catalytic agents that will retain the efficiency, specificity, and environmental-friendliness of natural enzymes. Despite extensive efforts, there is still an unmet need for improved enzyme mimics and novel concepts to discover and optimize such agents. Inspired by the catalytic activity of amyloids and the formation of amyloid-like assemblies by metabolites, our group pioneered the development of novel metabolite-metal co-assemblies (bio-nanozymes) that produce nanomaterials mimicking the catalytic function of common metalloenzymes that are being used for various technological applications. In addition to their notable activity, bio-nanozymes are remarkably safe as they are purely composed of amino acids and minerals that are harmless to the environment. The bio-nanozymes exhibit high efficiency and exceptional robustness, even under extreme conditions of temperature, pH, and salinity that are impractical for enzymes. Our group has recently also demonstrated the formation of ordered amino acid co-assemblies showing selective and preferential interactions comparable to the organization of residues in folded proteins. The identified bio-nanozymes can be used in various applications including environmental remediation, synthesis of new materials, and green energy.
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Affiliation(s)
- Om Shanker Tiwari
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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4
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Wang D, Ingram AA, Okumura A, Spaniol TP, Schwaneberg U, Okuda J. Benzylic C(sp 3 )-H Bond Oxidation with Ketone Selectivity by a Cobalt(IV)-Oxo Embedded in a β-Barrel Protein. Chemistry 2024; 30:e202303066. [PMID: 37818668 DOI: 10.1002/chem.202303066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/12/2023]
Abstract
Artificial metalloenzymes have emerged as biohybrid catalysts that allow to combine the reactivity of a metal catalyst with the flexibility of protein scaffolds. This work reports the artificial metalloenzymes based on the β-barrel protein nitrobindin NB4, in which a cofactor [CoII X(Me3 TACD-Mal)]+ X- (X=Cl, Br; Me3 TACD=N,N' ,N''-trimethyl-1,4,7,10-tetraazacyclododecane, Mal=CH2 CH2 CH2 NC4 H2 O2 ) was covalently anchored via a Michael addition reaction. These biohybrid catalysts showed higher efficiency than the free cobalt complexes for the oxidation of benzylic C(sp3 )-H bonds in aqueous media. Using commercially available oxone (2KHSO5 ⋅ KHSO4 ⋅ K2 SO4 ) as oxidant, a total turnover number of up to 220 and 97 % ketone selectivity were achieved for tetralin. As catalytically active intermediate, a mononuclear terminal cobalt(IV)-oxo species [Co(IV)=O]2+ was generated by reacting the cobalt(II) cofactor with oxone in aqueous solution and characterized by ESI-TOF MS.
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Affiliation(s)
- Dong Wang
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Aaron A Ingram
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Akira Okumura
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Thomas P Spaniol
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074, Aachen, Germany
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5
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Marciesky M, Aga DS, Bradley IM, Aich N, Ng C. Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS). J Chem Inf Model 2023; 63:7299-7319. [PMID: 37981739 PMCID: PMC10716909 DOI: 10.1021/acs.jcim.3c01303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023]
Abstract
Per and polyfluoroalkyl substances (PFAS) present a unique challenge to remediation techniques because their strong carbon-fluorine bonds make them difficult to degrade. This review explores the use of in silico enzymatic design as a potential PFAS degradation technique. The scope of the enzymes included is based on currently known PFAS degradation techniques, including chemical redox systems that have been studied for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) defluorination, such as those that incorporate hydrated electrons, sulfate, peroxide, and metal catalysts. Bioremediation techniques are also discussed, namely the laccase and horseradish peroxidase systems. The redox potential of known reactants and enzymatic radicals/metal-complexes are then considered and compared to potential enzymes for degrading PFAS. The molecular structure and reaction cycle of prospective enzymes are explored. Current knowledge and techniques of enzyme design, particularly radical-generating enzymes, and application are also discussed. Finally, potential routes for bioengineering enzymes to enable or enhance PFAS remediation are considered as well as the future outlook for computational exploration of enzymatic in situ bioremediation routes for these highly persistent and globally distributed contaminants.
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Affiliation(s)
- Melissa Marciesky
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Diana S Aga
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Ian M Bradley
- Department of Civil, Structural, and Environmental Engineering, State University of New York at Buffalo, Buffalo, New York 14228, United States
- Research and Education in Energy, Environmental and Water (RENEW) Institute, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Nirupam Aich
- Department of Civil and Environmental Engineering, University of Nebraska─Lincoln, Lincoln, Nebraska 68588-0531, United States
| | - Carla Ng
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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6
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Diep P, Kell B, Yakunin A, Hilfinger A, Mahadevan R. Quantifying metal-binding specificity of CcNikZ-II from Clostridium carboxidivorans in the presence of competing metal ions. Anal Biochem 2023; 676:115182. [PMID: 37355028 DOI: 10.1016/j.ab.2023.115182] [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: 01/22/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 06/26/2023]
Abstract
Many proteins bind transition metal ions as cofactors to carry out their biological functions. Despite binding affinities for divalent transition metal ions being predominantly dictated by the Irving-Williams series for wild-type proteins, in vivo metal ion binding specificity is ensured by intracellular mechanisms that regulate free metal ion concentrations. However, a growing area of biotechnology research considers the use of metal-binding proteins in vitro to purify specific metal ions from wastewater, where specificity is dictated by the protein's metal binding affinities. A goal of metalloprotein engineering is to modulate these affinities to improve a protein's specificity towards a particular metal; however, the quantitative relationship between the affinities and the equilibrium metal-bound protein fractions depends on the underlying binding mechanisms. Here we demonstrate a high-throughput intrinsic tryptophan fluorescence quenching method to validate binding models in multi-metal solutions for CcNikZ-II, a nickel-binding protein from Clostridium carboxidivorans. Using our validated models, we quantify the relationship between binding affinity and specificity in different classes of metal-binding models for CcNikZ-II. We further illustrate the potential relevance of data-informed models to predicting engineering targets for improved specificity.
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Affiliation(s)
- Patrick Diep
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Brayden Kell
- Department of Physics, University of Toronto, Toronto, ON, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| | - Alexander Yakunin
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, UK
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ON, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada; Department of Mathematics, University of Toronto, Toronto, ON, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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7
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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8
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Wijker S, Palmans ARA. Protein-Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water. Chempluschem 2023; 88:e202300260. [PMID: 37417828 DOI: 10.1002/cplu.202300260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The folding of proteins into functional nanoparticles with defined 3D structures has inspired chemists to create simple synthetic systems mimicking protein properties. The folding of polymers into nanoparticles in water proceeds via different strategies, resulting in the global compaction of the polymer chain. Herein, we review the different methods available to control the conformation of synthetic polymers and collapse/fold them into structured, functional nanoparticles, such as hydrophobic collapse, supramolecular self-assembly, and covalent cross-linking. A comparison is made between the design principles of protein folding to synthetic polymer folding and the formation of structured nanocompartments in water, highlighting similarities and differences in design and function. We also focus on the importance of structure for functional stability and diverse applications in complex media and cellular environments.
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Affiliation(s)
- Stefan Wijker
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
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9
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Kinugawa T, Matsuo T. Reactivity regulation for olefin metathesis-catalyzing ruthenium complexes with sulfur atoms at the terminal of 2-alkoxybenzylidene ligands. Dalton Trans 2023. [PMID: 37368438 DOI: 10.1039/d3dt01471a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
For regulating the olefin metathesis (OM) activity of the Hoveyda-Grubbs second-generation complex (HG-II), the structural modification of the benzylidene ligand is a useful strategy. This paper reports the effect of a chalcogen atom placed at the end of the benzylidene group on the catalytic properties of HG-II derivatives, using complexes with a thioether or ether component in the benzylidene ligand (ortho-Me-E-(CH2)2O-styrene; E = S, O). Nuclear magnetic resonance and X-ray crystallographic analyses of the complex with a thioether moiety (E = S) proved the (O,S)-bidentate and trans-dichlorido coordination for the complex. A stoichiometric ligand exchange between HG-II and the benzylidene ligand (E = S) produced the corresponding complex with an 86% yield, confirming higher stability of the complex (E = S) than that of HG-II. Despite the bidentate chelation, the complex (E = S) exhibited OM catalytic activity, indicating the exchangeability of the S-chelating ligand with an olefinic substrate. The green solution color, a characteristic of HG-II derivatives, was retained after the complex (E = S)-mediated OM reactions, indicating high catalyst durability. Conversely, the complex (E = O) rapidly initiated OM reactions; however, it showed low catalyst durability. In the OM reactions conducted in the presence of methanol, the complex (E = S) exhibited higher yields than the complex (E = O) and HG-II: the S-coordination increased the catalyst tolerance to methanol. A coordinative atom (such as sulfur) placed at the terminal of the benzylidene ligand can precisely regulate the reactivity of HG-II derivatives.
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Affiliation(s)
- Tsubasa Kinugawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan.
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan.
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10
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Sauer DF, Markel U, Schiffels J, Okuda J, Schwaneberg U. FhuA: From Iron-Transporting Transmembrane Protein to Versatile Scaffolds through Protein Engineering. Acc Chem Res 2023. [PMID: 37191525 DOI: 10.1021/acs.accounts.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
ConspectusProtein engineering has emerged as a powerful methodology to tailor the properties of proteins. It empowers the design of biohybrid catalysts and materials, thereby enabling the convergence of materials science, chemistry, and medicine. The choice of a protein scaffold is an important factor for performance and potential applications. In the past two decades, we utilized the ferric hydroxamate uptake protein FhuA. FhuA is, from our point of view, a versatile scaffold due to its comparably large cavity and robustness toward temperature as well as organic cosolvents. FhuA is a natural iron transporter located in the outer membrane of Escherichia coli (E. coli). Wild-type FhuA consists of 714 amino acids and has a β-barrel structure composed of 22 antiparallel β-sheets, closed by an internal globular "cork" domain (amino acids 1-160). FhuA is robust in a broad pH range and toward organic cosolvents; therefore, we envisioned FhuA to be a suitable platform for various applications in (i) biocatalysis, (ii) materials science, and (iii) the construction of artificial metalloenzymes.(i) Applications in biocatalysis were achieved by removing the globular cork domain (FhuA_Δ1-160), thereby creating a large pore for the passive transport of otherwise difficult-to-import molecules through diffusion. Introducing this FhuA variant into the outer membrane of E. coli facilitates the uptake of substrates for downstream biocatalytic conversion. Furthermore, removing the globular "cork" domain without structural collapse of the ß-barrel protein allowed the use of FhuA as a membrane filter, exhibiting a preference for d-arginine over l-arginine.(ii) FhuA is a transmembrane protein, which makes it attractive to be used for applications in non-natural polymeric membranes. Inserting FhuA into polymer vesicles yielded so-called synthosomes (i.e., catalytic synthetic vesicles in which the transmembrane protein acted as a switchable gate or filter). Our work in this direction enables polymersomes to be used in biocatalysis, DNA recovery, and the controlled (triggered) release of molecules. Furthermore, FhuA can be used as a building block to create protein-polymer conjugates to generate membranes.(iii) Artificial metalloenzymes (ArMs) are formed by incorporating a non-native metal ion or metal complex into a protein. This combines the best of two worlds: the vast reaction and substrate scope of chemocatalysis and the selectivity and evolvability of enzymes. With its large inner diameter, FhuA can harbor (bulky) metal catalysts. Among others, we covalently attached a Grubbs-Hoveyda-type catalyst for olefin metathesis to FhuA. This artificial metathease was then used in various chemical transformations, ranging from polymerizations (ring-opening metathesis polymerization) to enzymatic cascades involving cross-metathesis. Ultimately, we generated a catalytically active membrane by copolymerizing FhuA and pyrrole. The resulting biohybrid material was then equipped with the Grubbs-Hoveyda-type catalyst and used in ring-closing metathesis.The number of reports on FhuA and its various applications indicates that it is a versatile building block to generate hybrid catalysts and materials. We hope that our research will inspire future research efforts at the interface of biotechnology, catalysis, and material science in order to create biohybrid systems that offer smart solutions for current challenges in catalysis, material science, and medicine.
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Affiliation(s)
- Daniel F Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Johannes Schiffels
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, D-52056, Aachen, Germany
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11
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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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12
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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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13
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Abstract
Chemoenzymatic catalysis, by definition, involves the merging of sequential reactions using both chemocatalysis and biocatalysis, typically in a single reaction vessel. A major challenge, the solution to which, however, is associated with numerous advantages, is to run such one-pot processes in water: the majority of enzyme-catalyzed processes take place in water as Nature's reaction medium, thus enabling a broad synthetic diversity when using water due to the option to use virtually all types of enzymes. Furthermore, water is cheap, abundantly available, and environmentally friendly, thus making it, in principle, an ideal reaction medium. On the other hand, most chemocatalysis is routinely performed today in organic solvents (which might deactivate enzymes), thus appearing to make it difficult to combine such reactions with biocatalysis toward one-pot cascades in water. Several creative approaches and solutions that enable such combinations of chemo- and biocatalysis in water to be realized and applied to synthetic problems are presented herein, reflecting the state-of-the-art in this blossoming field. Coverage has been sectioned into three parts, after introductory remarks: (1) Chapter 2 focuses on historical developments that initiated this area of research; (2) Chapter 3 describes key developments post-initial discoveries that have advanced this field; and (3) Chapter 4 highlights the latest achievements that provide attractive solutions to the main question of compatibility between biocatalysis (used predominantly in aqueous media) and chemocatalysis (that remains predominantly performed in organic solvents), both Chapters covering mainly literature from ca. 2018 to the present. Chapters 5 and 6 provide a brief overview as to where the field stands, the challenges that lie ahead, and ultimately, the prognosis looking toward the future of chemoenzymatic catalysis in organic synthesis.
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Affiliation(s)
- Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Fabrice Gallou
- Chemical & Analytical Development, Novartis Pharma AG, 4056Basel, Switzerland
| | - Bruce H Lipshutz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California93106, United States
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14
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Yang X, Wu W, Chen X, Wu F, Fan S, Yu P, Mao L. A versatile artificial metalloenzyme scaffold enabling direct bioelectrocatalysis in solution. SCIENCE ADVANCES 2022; 8:eabo3315. [PMID: 36322668 PMCID: PMC9629707 DOI: 10.1126/sciadv.abo3315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Artificial metalloenzymes (ArMs) are commonly designed with protein scaffolds containing buried coordination pockets to achieve substrate specificity and product selectivity for homogeneous reactions. However, their reactivities toward heterogeneous transformations are limited because interfacial electron transfers are hampered by the backbone shells. Here, we introduce bacterial small laccase (SLAC) as a new protein scaffold for constructing ArMs to directly catalyze electrochemical transformations. We use molecular dynamics simulation, x-ray crystallography, spectroscopy, and computation to illustrate the scaffold-directed assembly of an oxo-bridged dicobalt motif on protein surface. The resulting ArM in aqueous phase catalyzes electrochemical water oxidation without mediators or electrode modifications. Mechanistic investigation reveals the role of SLAC scaffold in defining the four-electron transfer pathway from water to oxygen. Furthermore, we demonstrate that SLAC-based ArMs implemented with Ni2+, Mn2+, Ru3+, Pd2+, or Ir3+ also enable direct bioelectrocatalysis of water electrolysis. Our study provides a versatile and generalizable route to complement heterogeneous repertoire of ArMs for expanded applications.
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Affiliation(s)
- Xiaoti Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Chen
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilong Fan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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15
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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16
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Prakash D, Mitra S, Murphy M, Chakraborty S. Oxidation and Peroxygenation of C–H Bonds by Artificial Cu Peptides (ArCuPs): Improved Catalysis via Selective Outer Sphere Modifications. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Divyansh Prakash
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Suchitra Mitra
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Morgan Murphy
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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17
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Gu Y, Bloomer BJ, Liu Z, Chen R, Clark DS, Hartwig JF. Directed Evolution of Artificial Metalloenzymes in Whole Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yang Gu
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
- Present address: CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Brandon J. Bloomer
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Zhennan Liu
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Reichi Chen
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering University of California Berkeley CA 94720 USA
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - John F. Hartwig
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
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18
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Gu Y, Bloomer BJ, Liu Z, Chen R, Clark DS, Hartwig JF. Directed Evolution of Artificial Metalloenzymes in Whole Cells. Angew Chem Int Ed Engl 2022; 61:e202110519. [PMID: 34766418 PMCID: PMC9707807 DOI: 10.1002/anie.202110519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/15/2021] [Indexed: 01/28/2023]
Abstract
Artificial metalloenzymes (ArMs), created by introducing synthetic cofactors into protein scaffolds, are an emerging class of catalyst for non-natural reactions. Although many classes of ArMs are known, in vitro reconstitution of cofactors and proteins has been a limiting step in the high-throughput screening and directed evolution of ArMs because purification of individual host proteins is time-consuming. We describe the application of a platform to combine mutants of the P450 enzyme CYP119 and the cofactor Ir(Me)MPIX in vivo, by coexpression of the CYP119 mutants with the heme transporter encoded by the hug operon, to the directed evolution of ArMs containing Ir(Me)MPIX in whole cells. We applied this platform to the development an ArMs catalyzing the insertion of the acyclic carbene from α-diazopropanoate esters (Me-EDA) into the N-H bonds of N-alkyl anilines, a combination of carbene and amine classes for which mutant enzymes of natural hemoproteins previously reacted with low enantioselectivity. The mutants of the artificial metalloenzyme Ir(Me)CYP119 identified by an evolution campaign involving more than 4000 mutants are shown to catalyze the reaction of Me-EDA with N-methyl anilines to form chiral chiral amino esters with high TON and good enantioselectivity, thereby demonstrating that the directed evolution of ArMs can rival that of natural enzymes in vivo.
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Affiliation(s)
- Yang Gu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Present address: CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Brandon J Bloomer
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Zhennan Liu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Reichi Chen
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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19
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Liu Z, Huang J, Gu Y, Clark DS, Mukhopadhyay A, Keasling JD, Hartwig JF. Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C─H and C═C Bonds. J Am Chem Soc 2022; 144:883-890. [PMID: 34985270 DOI: 10.1021/jacs.1c10975] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. We show that a non-pathogenic E. coli strain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivo catalyzes carbene insertions into benzylic C-H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.
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Affiliation(s)
- Zhennan Liu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
| | - Yang Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aindrila Mukhopadhyay
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Department of Bioengineering, University of California, Berkeley, California 94720, United States.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, China.,Center for Biosustainability, Danish Technical University, Lyngby 2800 Kgs, Denmark
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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20
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Nasibullin I, Smirnov I, Ahmadi P, Vong K, Kurbangalieva A, Tanaka K. Synthetic prodrug design enables biocatalytic activation in mice to elicit tumor growth suppression. Nat Commun 2022; 13:39. [PMID: 35013295 PMCID: PMC8748823 DOI: 10.1038/s41467-021-27804-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Considering the intrinsic toxicities of transition metals, their incorporation into drug therapies must operate at minimal amounts while ensuring adequate catalytic activity within complex biological systems. As a way to address this issue, this study investigates the design of synthetic prodrugs that are not only tuned to be harmless, but can be robustly transformed in vivo to reach therapeutically relevant levels. To accomplish this, retrosynthetic prodrug design highlights the potential of naphthylcombretastatin-based prodrugs, which form highly active cytostatic agents via sequential ring-closing metathesis and aromatization. Structural adjustments will also be done to improve aspects related to catalytic reactivity, intrinsic bioactivity, and hydrolytic stability. The developed prodrug therapy is found to possess excellent anticancer activities in cell-based assays. Furthermore, in vivo activation by intravenously administered glycosylated artificial metalloenzymes can also induce significant reduction of implanted tumor growth in mice.
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Affiliation(s)
- Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Ivan Smirnov
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya street, Kazan, 420008, Russia
| | - Peni Ahmadi
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Kenward Vong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Almira Kurbangalieva
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya street, Kazan, 420008, Russia
| | - Katsunori Tanaka
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya street, Kazan, 420008, Russia.
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8552, Japan.
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21
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Stein A, Chen D, Igareta NV, Cotelle Y, Rebelein JG, Ward TR. A Dual Anchoring Strategy for the Directed Evolution of Improved Artificial Transfer Hydrogenases Based on Carbonic Anhydrase. ACS CENTRAL SCIENCE 2021; 7:1874-1884. [PMID: 34849402 PMCID: PMC8620556 DOI: 10.1021/acscentsci.1c00825] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Artificial metalloenzymes result from anchoring a metal cofactor within a host protein. Such hybrid catalysts combine the selectivity and specificity of enzymes with the versatility of (abiotic) transition metals to catalyze new-to-nature reactions in an evolvable scaffold. With the aim of improving the localization of an arylsulfonamide-bearing iridium-pianostool catalyst within human carbonic anhydrase II (hCAII) for the enantioselective reduction of prochiral imines, we introduced a covalent linkage between the host and the guest. Herein, we show that a judiciously positioned cysteine residue reacts with a p-nitropicolinamide ligand bound to iridium to afford an additional sulfonamide covalent linkage. Three rounds of directed evolution, performed on the dually anchored cofactor, led to improved activity and selectivity for the enantioselective reduction of harmaline (up to 97% ee (R) and >350 turnovers on a preparative scale). To evaluate the substrate scope, the best hits of each generation were tested with eight substrates. X-ray analysis, carried out at various stages of the evolutionary trajectory, was used to scrutinize (i) the nature of the covalent linkage between the cofactor and the host as well as (ii) the remodeling of the substrate-binding pocket.
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Affiliation(s)
- Alina Stein
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| | - Dongping Chen
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| | - Nico V. Igareta
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| | - Yoann Cotelle
- Aix-Marseille
Université, CNRS, Centrale Marseille, iSm2, 13284 Marseille, France
| | - Johannes G. Rebelein
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
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22
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23
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Baiyoumy A, Vallapurackal J, Schwizer F, Heinisch T, Kardashliev T, Held M, Panke S, Ward TR. Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein. ACS Catal 2021; 11:10705-10712. [PMID: 34504734 PMCID: PMC8419837 DOI: 10.1021/acscatal.1c02405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/26/2021] [Indexed: 12/14/2022]
Abstract
Artificial metalloenzymes (ArMs) combine characteristics of both homogeneous catalysts and enzymes. Merging abiotic and biotic features allows for the implementation of new-to-nature reactions in living organisms. Here, we present the directed evolution of an artificial metalloenzyme based on Escherichia coli surface-displayed streptavidin (SavSD hereafter). Through the binding of a ruthenium-pianostool cofactor to SavSD, an artificial allylic deallylase (ADAse hereafter) is assembled, which displays catalytic activity toward the deprotection of alloc-protected 3-hydroxyaniline. The uncaged aminophenol acts as a gene switch and triggers the overexpression of a fluorescent green fluorescent protein (GFP) reporter protein. This straightforward readout of ADAse activity allowed the simultaneous saturation mutagenesis of two amino acid residues in Sav near the ruthenium cofactor, expediting the screening of 2762 individual clones. A 1.7-fold increase of in vivo activity was observed for SavSD S112T-K121G compared to the wild-type SavSD (wt-SavSD). Finally, the best performing Sav isoforms were purified and tested in vitro (SavPP hereafter). For SavPP S112M-K121A, a total turnover number of 372 was achieved, corresponding to a 5.9-fold increase vs wt-SavPP. To analyze the marked difference in activity observed between the surface-displayed and purified ArMs, the oligomeric state of SavSD was determined. For this purpose, crosslinking experiments of E. coli cells overexpressing SavSD were carried out, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot. The data suggest that SavSD is most likely displayed as a monomer on the surface of E. coli. We hypothesize that the difference between the in vivo and in vitro screening results may reflect the difference in the oligomeric state of SavSD vs soluble SavPP (monomeric vs tetrameric). Accordingly, care should be applied when evolving oligomeric proteins using E. coli surface display.
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Affiliation(s)
- Alain Baiyoumy
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Jaicy Vallapurackal
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Fabian Schwizer
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Tillmann Heinisch
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | | | - Martin Held
- ETH
Zürich, D-BSSE, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sven Panke
- ETH
Zürich, D-BSSE, Mattenstrasse 26, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
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24
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Leveson-Gower R, Zhou Z, Drienovská I, Roelfes G. Unlocking Iminium Catalysis in Artificial Enzymes to Create a Friedel-Crafts Alkylase. ACS Catal 2021; 11:6763-6770. [PMID: 34168902 PMCID: PMC8218303 DOI: 10.1021/acscatal.1c00996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/10/2021] [Indexed: 02/08/2023]
Abstract
The construction and engineering of artificial enzymes consisting of abiological catalytic moieties incorporated into protein scaffolds is a promising strategy to realize non-natural mechanisms in biocatalysis. Here, we show that incorporation of the noncanonical amino acid para-aminophenylalanine (pAF) into the nonenzymatic protein scaffold LmrR creates a proficient and stereoselective artificial enzyme (LmrR_pAF) for the vinylogous Friedel-Crafts alkylation between α,β-unsaturated aldehydes and indoles. pAF acts as a catalytic residue, activating enal substrates toward conjugate addition via the formation of intermediate iminium ion species, while the protein scaffold provides rate acceleration and stereoinduction. Improved LmrR_pAF variants were identified by low-throughput directed evolution advised by alanine-scanning to obtain a triple mutant that provided higher yields and enantioselectivities for a range of aliphatic enals and substituted indoles. Analysis of Michaelis-Menten kinetics of LmrR_pAF and evolved mutants reveals that different activities emerge via evolutionary pathways that diverge from one another and specialize catalytic reactivity. Translating this iminium-based catalytic mechanism into an enzymatic context will enable many more biocatalytic transformations inspired by organocatalysis.
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Affiliation(s)
- Reuben
B. Leveson-Gower
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Zhi Zhou
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | | | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
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25
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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26
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Markel U, Sauer DF, Wittwer M, Schiffels J, Cui H, Davari MD, Kröckert KW, Herres-Pawlis S, Okuda J, Schwaneberg U. Chemogenetic Evolution of a Peroxidase-like Artificial Metalloenzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Daniel F. Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Malte Wittwer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Johannes Schiffels
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Konstantin W. Kröckert
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Sonja Herres-Pawlis
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI—Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
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27
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Nguyen H, Kleingardner J. Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering. Protein Sci 2021; 30:1247-1257. [PMID: 33829594 DOI: 10.1002/pro.4074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/03/2023]
Abstract
Metal cofactors within proteins perform a versatile set of essential cellular functions. In order to take advantage of the diverse functionality of metalloproteins, researchers have been working to design or modify metal binding sites in proteins to rationally tune the function or activity of the metal cofactor. This study has performed an analysis on the backbone atom geometries of metal-binding amino acids among 10 different metal binding sites within the entire protein data bank. A set of 13 geometric parameters (features) was identified that is capable of predicting the presence of a metal cofactor in the protein structure with overall accuracies of up to 97% given only the relative positions of their backbone atoms. The decision tree machine-learning algorithm used can quickly analyze an entire protein structure for the presence of sets of primary metal coordination spheres upon mutagenesis, independent of their original amino acid identities. The methodology was designed for application in the field of metalloprotein engineering. A cluster analysis using the data set was also performed and demonstrated that the features chosen are useful for identifying clusters of structurally similar metal-binding sites.
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Affiliation(s)
- Hoang Nguyen
- Department of Computer Science, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jesse Kleingardner
- Department of Chemistry and Biochemistry, Messiah University, Mechanicsburg, Pennsylvania, USA
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28
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Thiel A, Sauer DF, Markel U, Mertens MAS, Polen T, Schwaneberg U, Okuda J. An artificial ruthenium-containing β-barrel protein for alkene-alkyne coupling reaction. Org Biomol Chem 2021; 19:2912-2916. [PMID: 33735355 DOI: 10.1039/d1ob00279a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A modified Cp*Ru complex, equipped with a maleimide group, was covalently attached to a cysteine of an engineered variant of Ferric hydroxamate uptake protein component: A (FhuA). This synthetic metalloprotein catalyzed the intermolecular alkene-alkyne coupling of 3-butenol with 5-hexynenitrile. When compared with the protein-free Cp*Ru catalyst, the biohybrid catalyst produced the linear product with higher regioselectivity.
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Affiliation(s)
- Andreas Thiel
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany.
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29
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Chordia S, Narasimhan S, Lucini Paioni A, Baldus M, Roelfes G. In Vivo Assembly of Artificial Metalloenzymes and Application in Whole-Cell Biocatalysis*. Angew Chem Int Ed Engl 2021; 60:5913-5920. [PMID: 33428816 PMCID: PMC7986609 DOI: 10.1002/anie.202014771] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Indexed: 12/14/2022]
Abstract
We report the supramolecular assembly of artificial metalloenzymes (ArMs), based on the Lactococcal multidrug resistance regulator (LmrR) and an exogeneous copper(II)-phenanthroline complex, in the cytoplasm of E. coli cells. A combination of catalysis, cell-fractionation, and inhibitor experiments, supplemented with in-cell solid-state NMR spectroscopy, confirmed the in-cell assembly. The ArM-containing whole cells were active in the catalysis of the enantioselective Friedel-Crafts alkylation of indoles and the Diels-Alder reaction of azachalcone with cyclopentadiene. Directed evolution resulted in two different improved mutants for both reactions, LmrR_A92E_M8D and LmrR_A92E_V15A, respectively. The whole-cell ArM system required no engineering of the microbial host, the protein scaffold, or the cofactor to achieve ArM assembly and catalysis. We consider this a key step towards integrating abiological catalysis with biosynthesis to generate a hybrid metabolism.
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Affiliation(s)
- Shreyans Chordia
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
- Current address: Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| | - Alessandra Lucini Paioni
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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30
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Klein AS, Zeymer C. Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis. Protein Eng Des Sel 2021; 34:6150309. [PMID: 33635315 DOI: 10.1093/protein/gzab003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.
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Affiliation(s)
- Andreas S Klein
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
| | - Cathleen Zeymer
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
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31
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Chordia S, Narasimhan S, Lucini Paioni A, Baldus M, Roelfes G. In Vivo Assembly of Artificial Metalloenzymes and Application in Whole‐Cell Biocatalysis**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014771] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shreyans Chordia
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Current address: Structural and Computational Biology Unit European Molecular Biology Laboratory Meyerhofstraße 1 69117 Heidelberg Germany
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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32
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Fu Y, Huang J, Wu Y, Liu X, Zhong F, Wang J. Biocatalytic Cross-Coupling of Aryl Halides with a Genetically Engineered Photosensitizer Artificial Dehalogenase. J Am Chem Soc 2021; 143:617-622. [PMID: 33410683 DOI: 10.1021/jacs.0c10882] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Devising artificial photoenzymes for abiological bond-forming reactions is of high synthetic value but also a tremendous challenge. Disclosed herein is the first photobiocatalytic cross-coupling of aryl halides enabled by a designer artificial dehalogenase, which features a genetically encoded benzophenone chromophore and site-specifically modified synthetic NiII(bpy) cofactor with tunable proximity to streamline the dual catalysis. Transient absorption studies suggest the likelihood of energy transfer activation in the elementary organometallic event. This design strategy is viable to significantly expand the catalytic repertoire of artificial photoenzymes for useful organic transformations.
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Affiliation(s)
- Yu Fu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology (HUST), 1037 Luoyu Road, Wuhan 430074, P.R. China.,Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Beijing 100020, P.R. China
| | - Jian Huang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Beijing 100020, P.R. China
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology (HUST), 1037 Luoyu Road, Wuhan 430074, P.R. China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Beijing 100020, P.R. China
| | - Fangrui Zhong
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology (HUST), 1037 Luoyu Road, Wuhan 430074, P.R. China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Beijing 100020, P.R. China
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33
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Construction of a whole-cell biohybrid catalyst using a Cp*Rh(III)-dithiophosphate complex as a precursor of a metal cofactor. J Inorg Biochem 2021; 216:111352. [PMID: 33461020 DOI: 10.1016/j.jinorgbio.2020.111352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/01/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022]
Abstract
A whole-cell biohybrid catalyst where a (pentamethylcyclopentadienyl)rhodium(III) (Cp*Rh(III)) complex was covalently incorporated into the cavity of nitrobindin (NB), a β-barrel protein, was prepared on an E. coli cell surface to produce isoquinolines via C(sp2)-H bond activation. In this whole-cell biohybrid system, the Cp*Rh(III)-dithiophosphate complex with latent catalytic activity was utilized as a precursor of the metal cofactor. Strong chelation of the dithiophosphate ligands protects the rhodium complex from being deactivated by abundant nucleophiles in cellular environments during conjugation of the cofactor with the protein scaffold. The whole-cell biohybrid catalyst was then activated upon addition of Ag+ ion to dissociate the dithiophosphate ligands and promoted cycloaddition of acetophenone oxime with diphenylacetylene. Furthermore, the activity of the Cp*Rh(III)-linked whole-cell biohybrid catalyst was enhanced 2.1-fold by introducing glutamate residues at positions adjacent to the Cp*Rh(III) cofactor. These results indicate that the use of the Cp*Rh(III)-dithiophosphate complex with switchable activity from a "latent" form to an "active" form provides a new strategy for generating whole-cell biohybrid catalysts.
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34
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Vornholt T, Christoffel F, Pellizzoni MM, Panke S, Ward TR, Jeschek M. Systematic engineering of artificial metalloenzymes for new-to-nature reactions. SCIENCE ADVANCES 2021; 7:eabe4208. [PMID: 33523952 DOI: 10.1126/sciadv.abe4208] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Artificial metalloenzymes (ArMs) catalyzing new-to-nature reactions could play an important role in transitioning toward a sustainable economy. While ArMs have been created for various transformations, attempts at their genetic optimization have been case specific and resulted mostly in modest improvements. To realize their full potential, methods to rapidly discover active ArM variants for ideally any reaction of interest are required. Here, we introduce a reaction-independent, automation-compatible platform, which relies on periplasmic compartmentalization in Escherichia coli to rapidly and reliably engineer ArMs based on the biotin-streptavidin technology. We systematically assess 400 ArM mutants for five bioorthogonal transformations involving different metals, reaction mechanisms, and reactants, which include novel ArMs for gold-catalyzed hydroamination and hydroarylation. Activity enhancements up to 15-fold highlight the potential of the systematic approach. Furthermore, we suggest smart screening strategies and build machine learning models that accurately predict ArM activity from sequence, which has crucial implications for future ArM development.
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Affiliation(s)
- Tobias Vornholt
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Fadri Christoffel
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Michela M Pellizzoni
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Thomas R Ward
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Markus Jeschek
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland.
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
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35
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Sauer DF, Wittwer M, Markel U, Minges A, Spiertz M, Schiffels J, Davari MD, Groth G, Okuda J, Schwaneberg U. Chemogenetic engineering of nitrobindin toward an artificial epoxygenase. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00609f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemogenetic engineering turned the heme protein nitrobindin into an artificial epoxygenase: MnPPIX was introduced and subsequent protein engineering increased the activity in the epoxidation of styrene derivatives by overall 7-fold.
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Affiliation(s)
- Daniel F. Sauer
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Malte Wittwer
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Markel
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Alexander Minges
- Institute of Biochemical Plant Physiology
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Markus Spiertz
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | | | - Mehdi D. Davari
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Georg Groth
- Institute of Biochemical Plant Physiology
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI – Leibniz Institute for Interactive Materials
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36
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Nöth M, Hussmann L, Belthle T, El-Awaad I, Davari MD, Jakob F, Pich A, Schwaneberg U. MicroGelzymes: pH-Independent Immobilization of Cytochrome P450 BM3 in Microgels. Biomacromolecules 2020; 21:5128-5138. [PMID: 33206503 DOI: 10.1021/acs.biomac.0c01262] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Microgels are an emerging class of "ideal" enzyme carriers because of their chemical and process stability, biocompatibility, and high enzyme loading capability. In this work, we synthesized a new type of permanently positively charged poly(N-vinylcaprolactam) (PVCL) microgel with 1-vinyl-3-methylimidazolium (quaternization of nitrogen by methylation of N-vinylimidazole moieties) as a comonomer (PVCL/VimQ) through precipitation polymerization. The PVCL/VimQ microgels were characterized with respect to their size, charge, swelling degree, and temperature responsiveness in aqueous solutions. P450 monooxygenases are usually challenging to immobilize, and often, high activity losses occur after the immobilization (in the case of P450 BM3 from Bacillus megaterium up to 100% loss of activity). The electrostatic immobilization of P450 BM3 in permanently positively charged PVCL/VimQ microgels was achieved without the loss of catalytic activity at the pH optimum of P450 BM3 (pH 8; ∼9.4 nmol 7-hydroxy-3-carboxy coumarin ethyl ester/min for free and immobilized P450 BM3); the resulting P450-microgel systems were termed P450 MicroGelzymes (P450 μ-Gelzymes). In addition, P450 μ-Gelzymes offer the possibility of reversible ionic strength-triggered release and re-entrapment of the biocatalyst in processes (e.g., for catalyst reuse). Finally, a characterization of the potential of P450 μ-Gelzymes to provide resistance against cosolvents (acetonitrile, dimethyl sulfoxide, and 2-propanol) was performed to evaluate the biocatalytic application potential.
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Affiliation(s)
- Maximilian Nöth
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany
| | - Larissa Hussmann
- DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany.,Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Thomke Belthle
- DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany.,Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Islam El-Awaad
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany.,Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Felix Jakob
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany
| | - Andrij Pich
- DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany.,Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany.,Aachen Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials e.V., Forckenbeckstraβe 50, 52074 Aachen, Germany
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37
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Kato S, Onoda A, Taniguchi N, Schwaneberg U, Hayashi T. Directed Evolution of a Cp*Rh III -Linked Biohybrid Catalyst Based on a Screening Platform with Affinity Purification. Chembiochem 2020; 22:679-685. [PMID: 33026156 PMCID: PMC7894531 DOI: 10.1002/cbic.202000681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Directed evolution of Cp*RhIII‐linked nitrobindin (NB), a biohybrid catalyst, was performed based on an in vitro screening approach. A key aspect of this effort was the establishment of a high‐throughput screening (HTS) platform that involves an affinity purification step employing a starch‐agarose resin for a maltose binding protein (MBP) tag. The HTS platform enables efficient preparation of the purified MBP‐tagged biohybrid catalysts in a 96‐well format and eliminates background influence of the host E. coli cells. Three rounds of directed evolution and screening of more than 4000 clones yielded a Cp*RhIII‐linked NB(T98H/L100K/K127E) variant with a 4.9‐fold enhanced activity for the cycloaddition of acetophenone oximes with alkynes. It is confirmed that this HTS platform for directed evolution provides an efficient strategy for generating highly active biohybrid catalysts incorporating a synthetic metal cofactor.
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Affiliation(s)
- Shunsuke Kato
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akira Onoda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Naomasa Taniguchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen, 52074, Germany
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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38
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Villarino L, Chordia S, Alonso-Cotchico L, Reddem E, Zhou Z, Thunnissen AMWH, Maréchal JD, Roelfes G. Cofactor Binding Dynamics Influence the Catalytic Activity and Selectivity of an Artificial Metalloenzyme. ACS Catal 2020; 10:11783-11790. [PMID: 33101759 PMCID: PMC7574625 DOI: 10.1021/acscatal.0c01619] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/11/2020] [Indexed: 12/20/2022]
Abstract
We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits dynamics involving the positioning of its abiological metal cofactor. The position of the cofactor, in turn, was found to be related to the preferred catalytic reactivity, which is either the enantioselective Friedel-Crafts alkylation of indoles with β-substituted enones or the tandem Friedel-Crafts alkylation/enantioselective protonation of indoles with α-substituted enones. The artificial metalloenzyme could be specialized for one of these catalytic reactions introducing a single mutation in the protein. The relation between cofactor dynamics and activity and selectivity in catalysis has not been described for natural enzymes and, to date, appears to be particular for artificial metalloenzymes.
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Affiliation(s)
- Lara Villarino
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Shreyans Chordia
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Lur Alonso-Cotchico
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Eswar Reddem
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Zhi Zhou
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Andy Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193,
Cerdanyola del Vallés, Barcelona, Spain
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Ma H, Zou J, Li X, Chen G, Dong Y. Homochiral Covalent Organic Frameworks for Asymmetric Catalysis. Chemistry 2020; 26:13754-13770. [DOI: 10.1002/chem.202001006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/21/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Hui‐Chao Ma
- College of Chemistry, Chemical Engineering and Materials Science Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University Jinan 250014 P.R. China
| | - Jie Zou
- College of Chemistry, Chemical Engineering and Materials Science Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University Jinan 250014 P.R. China
| | - Xue‐Tian Li
- College of Chemistry, Chemical Engineering and Materials Science Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University Jinan 250014 P.R. China
| | - Gong‐Jun Chen
- College of Chemistry, Chemical Engineering and Materials Science Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University Jinan 250014 P.R. China
| | - Yu‐Bin Dong
- College of Chemistry, Chemical Engineering and Materials Science Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University Jinan 250014 P.R. China
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40
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Kato S, Onoda A, Grimm AR, Tachikawa K, Schwaneberg U, Hayashi T. Incorporation of a Cp*Rh(III)-dithiophosphate Cofactor with Latent Activity into a Protein Scaffold Generates a Biohybrid Catalyst Promoting C(sp 2)-H Bond Functionalization. Inorg Chem 2020; 59:14457-14463. [PMID: 32914980 DOI: 10.1021/acs.inorgchem.0c02245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A Cp*Rh(III)-dithiophosphate cofactor with "latent" catalytic activity was developed to construct an artificial metalloenzyme representing a new type of biohybrid catalyst which is capable of promoting C(sp2)-H bond functionalization within the β-barrel structure of nitrobindin (NB). To covalently conjugate the Cp*Rh(III) cofactor into a specific position of the hydrophobic cavity of NB via a maleimide-Cys linkage, strong chelation of the dithiophosphate ligand is employed to protect the rhodium metal center against attack by nucleophilic amino acid residues in the protein. It is found that subsequent addition of the Ag+ ion induces dissociation of the dithiophosphate ligands, thereby activating the catalytic activity of the Cp*Rh(III) cofactor. The resulting "active" biohybrid catalyst promotes cycloaddition of acetophenone oxime with diphenylacetylene via C(sp2)-H bond activation. This catalytic activity is enhanced 2.3-fold with the introduction of two glutamate residues (A100E/L125E) adjacent to the Cp*Rh(III) cofactor. The Cp*Rh(III) cofactor with switchable activity from a "latent" form to an "active" form provides a new strategy for generating biohybrid catalysts incorporating a variety of highly reactive transition metal complexes specifically within its protein scaffolds.
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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
| | - Alexander R Grimm
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Kengo Tachikawa
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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41
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Zuo H, Qin J, Zhang W, Bashir MA, Yu Q, Zhao W, Wu G, Zhong F. Hemin-Catalyzed Oxidative Phenol-Hydrazone [3+3] Cycloaddition Enables Rapid Construction of 1,3,4-Oxadiazines. Org Lett 2020; 22:6911-6916. [PMID: 32830501 DOI: 10.1021/acs.orglett.0c02442] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Herein, we present a hemin-catalyzed oxidative phenol-hydrazone [3+3] cycloaddition that accommodates a broad spectrum of N-arylhydrazones, a class of less exploited 1,3-dipoles due to their significant Lewis basicity and weak tendency to undergo 1,2-prototropy to form azomethine imines. It renders expedient assembly of diversely functionalized 1,3,4-oxadiazines with excellent atom and step economy. Preliminary mechanistic studies point to the involvement of a one-electron oxidation pathway, which likely differs from the base-promoted aerobic oxidative scenario.
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Affiliation(s)
- Honghua Zuo
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Jingyang Qin
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Wentao Zhang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Muhammad Adnan Bashir
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Qile Yu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University, 3002 Lantian Road, Shenzhen 518118, China
| | - Guojiao Wu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Fangrui Zhong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
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42
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Hishikawa Y, Maity B, Ito N, Abe S, Lu D, Ueno T. Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage. CHEM LETT 2020. [DOI: 10.1246/cl.200217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuki Hishikawa
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Nozomi Ito
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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43
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Synergistic catalysis in an artificial enzyme by simultaneous action of two abiological catalytic sites. Nat Catal 2020. [DOI: 10.1038/s41929-019-0420-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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44
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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45
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Fischer J, Renn D, Quitterer F, Radhakrishnan A, Liu M, Makki A, Ghorpade S, Rueping M, Arold ST, Groll M, Eppinger J. Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Johannes Fischer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Dominik Renn
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | | | | | | | | | | - Stefan T. Arold
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
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46
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Wu S, Zhou Y, Rebelein JG, Kuhn M, Mallin H, Zhao J, Igareta NV, Ward TR. Breaking Symmetry: Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes. J Am Chem Soc 2019; 141:15869-15878. [PMID: 31509711 PMCID: PMC6805045 DOI: 10.1021/jacs.9b06923] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The biotin–streptavidin technology
has been extensively
exploited to engineer artificial metalloenzymes (ArMs) that catalyze
a dozen different reactions. Despite its versatility, the homotetrameric
nature of streptavidin (Sav) and the noncooperative binding of biotinylated
cofactors impose two limitations on the genetic optimization of ArMs:
(i) point mutations are reflected in all four subunits of Sav, and
(ii) the noncooperative binding of biotinylated cofactors to Sav may
lead to an erosion in the catalytic performance, depending on the
cofactor:biotin-binding site ratio. To address these challenges, we
report on our efforts to engineer a (monovalent) single-chain dimeric
streptavidin (scdSav) as scaffold for Sav-based ArMs. The versatility
of scdSav as host protein is highlighted for the asymmetric transfer
hydrogenation of prochiral imines using [Cp*Ir(biot-p-L)Cl] as cofactor. By capitalizing on a more precise genetic fine-tuning
of the biotin-binding vestibule, unrivaled levels of activity and
selectivity were achieved for the reduction of challenging prochiral
imines. Comparison of the saturation kinetic data and X-ray structures
of [Cp*Ir(biot-p-L)Cl]·scdSav with a structurally
related [Cp*Ir(biot-p-L)Cl]·monovalent scdSav
highlights the advantages of the presence of a single biotinylated
cofactor precisely localized within the biotin-binding vestibule of
the monovalent scdSav. The practicality of scdSav-based ArMs was illustrated
for the reduction of the salsolidine precursor (500 mM) to afford
(R)-salsolidine in 90% ee and >17 000 TONs.
Monovalent scdSav thus provides a versatile scaffold to evolve more
efficient ArMs for in vivo catalysis and large-scale applications.
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Affiliation(s)
- Shuke Wu
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Yi Zhou
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Johannes G Rebelein
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Miriam Kuhn
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Hendrik Mallin
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Jingming Zhao
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Nico V Igareta
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
| | - Thomas R Ward
- Department of Chemistry , University of Basel , BPR 1096, Mattenstrasse 24a , CH-4058 Basel , Switzerland
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47
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Perez-Rizquez C, Rodriguez-Otero A, Palomo JM. Combining enzymes and organometallic complexes: novel artificial metalloenzymes and hybrid systems for C-H activation chemistry. Org Biomol Chem 2019; 17:7114-7123. [PMID: 31294731 DOI: 10.1039/c9ob01091b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review describes the recent advances in the design of novel artificial metalloenzymes and their application in C-H activation reactions. The combination of enzymes and metal or organometallic complexes for the creation of new artificial metalloenzymes has represented a very exciting research line. In particular, the development of proteins with the ability to perform C-H functionalization presents a significant challenge. Here we discuss the development of these processes on natural metalloenzymes by using directed evolution, biotin-(strept)avidin technologies, photocatalytic hybrids or reconstitution of heme-protein technology.
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Affiliation(s)
- Carlos Perez-Rizquez
- Department of Biocatalysis, Institute of Catalysis (CSIC), Marie Curie 2, Cantoblanco, Campus UAM, 28049 Madrid, Spain.
| | - Alba Rodriguez-Otero
- Department of Biocatalysis, Institute of Catalysis (CSIC), Marie Curie 2, Cantoblanco, Campus UAM, 28049 Madrid, Spain.
| | - Jose M Palomo
- Department of Biocatalysis, Institute of Catalysis (CSIC), Marie Curie 2, Cantoblanco, Campus UAM, 28049 Madrid, Spain.
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48
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Rebelein JG, Cotelle Y, Garabedian B, Ward TR. Chemical Optimization of Whole-Cell Transfer Hydrogenation Using Carbonic Anhydrase as Host Protein. ACS Catal 2019; 9:4173-4178. [PMID: 31080690 PMCID: PMC6503580 DOI: 10.1021/acscatal.9b01006] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/03/2019] [Indexed: 12/12/2022]
Abstract
![]()
Artificial
metalloenzymes combine a synthetic metallocofactor with
a protein scaffold and can catalyze abiotic reactions in vivo. Herein, we report on our efforts to valorize human carbonic anhydrase
II as a scaffold for whole-cell transfer hydrogenation. Two platforms
were tested: periplasmic compartmentalization and surface display
in Escherichia coli. A chemical optimization of an
IrCp* cofactor was performed. This led to 90 turnovers in the cell,
affording a 69-fold increase in periplasmic product formation over
the previously reported, sulfonamide-bearing IrCp* cofactor. These
findings highlight the versatility of carbonic anhydrase as a promising
scaffold for whole-cell catalysis with artificial metalloenzymes.
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Affiliation(s)
- Johannes G. Rebelein
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Yoann Cotelle
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Brett Garabedian
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
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49
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Papini C, Sommer C, Pecqueur L, Pramanik D, Roy S, Reijerse EJ, Wittkamp F, Artero V, Lubitz W, Fontecave M. Bioinspired Artificial [FeFe]-Hydrogenase with a Synthetic H-Cluster. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00540] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques, Collège de France−CNRS−Sorbonne Université, CNRS UMR 8229, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Constanze Sommer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France−CNRS−Sorbonne Université, CNRS UMR 8229, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA Fundamental Research Division, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Souvik Roy
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA Fundamental Research Division, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Edward J. Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Florian Wittkamp
- Inorganic Chemistry I, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA Fundamental Research Division, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France−CNRS−Sorbonne Université, CNRS UMR 8229, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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50
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Abstract
![]()
The biotechnological revolution has made it
possible to create
enzymes for many reactions by directed evolution. However, because
of the immense number of possibilities, the availability of enzymes
that possess a basal level of the desired catalytic activity is a
prerequisite for success. For new-to-nature reactions, artificial
metalloenzymes (ARMs), which are rationally designed hybrids of proteins
and catalytically active transition-metal complexes, can be such a
starting point. This Account details our efforts toward the
creation of ARMs for
the catalysis of new-to-nature reactions. Key to our approach is the
notion that the binding of substrates, that is, effective molarity,
is a key component to achieving large accelerations in catalysis.
For this reason, our designs are based on the multidrug resistance
regulator LmrR, a dimeric transcription factor with a large, hydrophobic
binding pocket at its dimer interface. In this pocket, there are two
tryptophan moieties, which are important for promiscuous binding of
planar hydrophobic conjugated compounds by π-stacking. The catalytic
machinery is introduced either by the covalent linkage of a catalytically
active metal complex or via the ligand or supramolecular assembly,
taking advantage of the two central tryptophan moieties for noncovalent
binding of transition-metal complexes. Designs based on the
chemical modification of LmrR were successful
in catalysis, but this approach proved too laborious to be practical.
Therefore, expanded genetic code methodologies were used to introduce
metal binding unnatural amino acids during LmrR biosynthesis in vivo.
These ARMs have been successfully applied in Cu(II) catalyzed Friedel–Crafts
alkylation of indoles. The extension to MDRs from the TetR family
resulted in ARMs capable of providing the opposite enantiomer of the
Friedel–Crafts product. We have employed a computationally
assisted redesign of these ARMs to create a more active and selective
artificial hydratase, introducing a glutamate as a general base at
a judicious position so it can activate and direct the incoming water
nucleophile. A supramolecularly assembled ARM from LmrR and
copper(II)–phenanthroline
was successful in Friedel–Crafts alkylation reactions, giving
rise to up to 94% ee. Also, hemin was bound, resulting in an artificial
heme enzyme for enantioselective cyclopropanation reactions. The importance
of structural dynamics of LmrR was suggested by computational studies,
which showed that the pore can open up to allow access of substrates
to the catalytic iron center, which, according to the crystal structure,
is deeply buried inside the protein. Finally, the assembly approaches
were combined to introduce both
a catalytic and a regulatory domain, resulting in an ARM that was
specifically activated in the presence of Fe(II) salts but not Zn(II)
salts. Our work demonstrates that LmrR is a privileged scaffold
for ARM
design: It allows for multiple assembly methods and even combinations
of these, it can be applied in a variety of different catalytic reactions,
and it shows significant structural dynamics that contribute to achieving
the desired catalytic activity. Moreover, both the creation via expanded
genetic code methods as well as the supramolecular assembly make LmrR-based
ARMs highly suitable for achieving the ultimate goal of the integration
of ARMs in biosynthetic pathways in vivo to create a hybrid metabolism.
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Affiliation(s)
- Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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