1
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Williams TL, Taily IM, Hatton L, Berezin AA, Wu YL, Moliner V, Świderek K, Tsai YH, Luk LYP. Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion. Angew Chem Int Ed Engl 2024; 63:e202403098. [PMID: 38545954 DOI: 10.1002/anie.202403098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Indexed: 04/20/2024]
Abstract
Secondary amines, due to their reactivity, can transform protein templates into catalytically active entities, accelerating the development of artificial enzymes. However, existing methods, predominantly reliant on modified ligands or N-terminal prolines, impose significant limitations on template selection. In this study, genetic code expansion was used to break this boundary, enabling secondary amines to be incorporated into alternative proteins and positions of choice. Pyrrolysine analogues carrying different secondary amines could be incorporated into superfolder green fluorescent protein (sfGFP), multidrug-binding LmrR and nucleotide-binding dihydrofolate reductase (DHFR). Notably, the analogue containing a D-proline moiety demonstrated both proteolytic stability and catalytic activity, conferring LmrR and DHFR with the desired transfer hydrogenation activity. While the LmrR variants were confined to the biomimetic 1-benzyl-1,4-dihydronicotinamide (BNAH) as the hydride source, the optimal DHFR variant favorably used the pro-R hydride from NADPH for stereoselective reactions (e.r. up to 92 : 8), highlighting that a switch of protein template could broaden the nucleophile option for catalysis. Owing to the cofactor compatibility, the DHFR-based secondary amine catalysis could be integrated into an enzymatic recycling scheme. This established method shows substantial potential in enzyme design, applicable from studies on enzyme evolution to the development of new biocatalysts.
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Affiliation(s)
- Thomas L Williams
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Irshad M Taily
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Lewis Hatton
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Andrey A Berezin
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Yi-Lin Wu
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Gaoke International Innovation Center, Guangming District, 518132, Shenzhen, Guangdong, China
| | - Louis Y P Luk
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
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2
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Wang L, Zhang M, Teng H, Wang Z, Wang S, Li P, Wu J, Yang L, Xu G. Rationally introducing non-canonical amino acids to enhance catalytic activity of LmrR for Henry reaction. BIORESOUR BIOPROCESS 2024; 11:26. [PMID: 38647789 PMCID: PMC10992053 DOI: 10.1186/s40643-024-00744-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/19/2024] [Indexed: 04/25/2024] Open
Abstract
The use of enzymes to catalyze Henry reaction has advantages of mild reaction conditions and low contamination, but low enzyme activity of promiscuous catalysis limits its application. Here, rational design was first performed to identify the key amino acid residues in Henry reaction catalyzed by Lactococcal multidrug resistance Regulator (LmrR). Further, non-canonical amino acids were introduced into LmrR, successfully obtaining variants that enhanced the catalytic activity of LmrR. The best variant, V15CNF, showed a 184% increase in enzyme activity compared to the wild type, and was 1.92 times more effective than the optimal natural amino acid variant, V15F. Additionally, this variant had a broad substrate spectrum, capable of catalyzing reactions between various aromatic aldehydes and nitromethane, with product yielded ranging from 55 to 99%. This study improved enzymatic catalytic activity by enhancing affinity between the enzyme and substrates, while breaking limited types of natural amino acid residues by introducing non-canonical amino acids into the enzyme, providing strategies for molecular modifications.
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Affiliation(s)
- Lan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Mengting Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Haidong Teng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhe Wang
- Huadong Medicine Co., Ltd, Hangzhou, 310011, Zhejiang, China
| | - Shulin Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Pengcheng Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
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3
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Fernandez-Lopez L, Cea-Rama I, Alvarez-Malmagro J, Ressmann AK, Gonzalez-Alfonso JL, Coscolín C, Shahgaldian P, Plou FJ, Modregger J, Pita M, Sanz-Aparicio J, Ferrer M. Transforming an esterase into an enantioselective catecholase through bioconjugation of a versatile metal-chelating inhibitor. Chem Commun (Camb) 2023. [PMID: 37376994 DOI: 10.1039/d3cc01946b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Metal complexes introduced into protein scaffolds can generate versatile biomimetic catalysts endowed with a variety of catalytic properties. Here, we synthesized and covalently bound a bipyridinyl derivative to the active centre of an esterase to generate a biomimetic catalyst that shows catecholase activity and enantioselective catalytic oxidation of (+)-catechin.
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Affiliation(s)
| | - Isabel Cea-Rama
- Instituto de Quimica Fisica Rocasolano (IQFR), CSIC, Madrid 28006, Spain
| | | | | | | | - Cristina Coscolín
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | - Patrick Shahgaldian
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Francisco J Plou
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | | | - Marcos Pita
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | | | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
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4
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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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5
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Wu L, Cheng L, Yang J, Yan Y, Zhang E, Kochovski Z, Li L, Wang Z, Deng L, Lu Y, Besenius P, Cui W, Chen G. Construction of Active Protein Materials: Manipulation on Morphology of Salmon Calcitonin Assemblies with Enhanced Bone Regeneration Effect. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2207526. [PMID: 36103707 DOI: 10.1002/adma.202207526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 06/15/2023]
Abstract
The effect of protein drugs is always limited by their relatively low stability and fast degradation property; thus, various elegant efforts have been made to improve the bioactivity and biocompatibility of the protein drugs. Here, an alternative way is proposed to solve this problem. By simply adding a limited amount of small-molecular regulator, which tunes the subtle balance of protein-protein interactions (PPIs) and disulfide bond formation, the self-assembly property of the protein drug can be regulated, forming an "active protein material" itself. This means that, the resulting biomaterial is dominated by the protein drug and water, with significantly enhanced bone regeneration effect compared to the virgin protein in vitro and in vivo, through multivalent effect between the protein and receptor and the retarded degradation of the assembled proteins. In this active protein material, the protein drug is not only the active drug, but also the drug carrier, which greatly increases the drug-loading efficiency of the biomaterial, indicating the advantages of the easy preparation, high efficiency, and low cost of the active protein material with a bright future in biomedical applications.
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Affiliation(s)
- Libin Wu
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Liang Cheng
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, P. R. China
| | - Jing Yang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Yufei Yan
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, P. R. China
| | - Ensong Zhang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Zdravko Kochovski
- Institute of Chemistry, University of Potsdam, 14476, Potsdam, Germany
- Institute of Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109, Berlin, Germany
| | - Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Zhen Wang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, P. R. China
| | - Lianfu Deng
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, P. R. China
| | - Yan Lu
- Institute of Chemistry, University of Potsdam, 14476, Potsdam, Germany
- Institute of Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109, Berlin, Germany
| | - Pol Besenius
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Wenguo Cui
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, P. R. China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 200433, P. R. China
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6
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Zhang N, Bessel P, Wu C. Copper-Containing Artificial Polyenzymes as a Clickase for Bioorthogonal Chemistry. Bioconjug Chem 2022; 33:1892-1899. [PMID: 36194410 DOI: 10.1021/acs.bioconjchem.2c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial polyenzymes (ArPoly) are tailored combinations of universal protein scaffolds and polymers newly proposed as promising alternatives to natural enzymes to expand the biocatalyst toolbox. The concept of ArPoly has been continuously extended to metal-containing ArPoly to overcome the drawbacks faced by conventional artificial metalloenzymes. Herein, we present a sustainable route to synthesize a novel water-soluble metalloenzyme for copper-catalyzed azide-alkyne cycloadditions in water with remarkable selectivity. In this case, synthetic l-proline monomers were polymerized onto bovine serum albumen in an aqueous medium via copper-mediated "grafting-from" atom-transfer radical polymerization, resulting in protein-polymer-copper conjugates named ArPolyclickase. The copper in ArPolyclickase plays pivotal bifunctional roles, not only as the catalyst for polymerization but also as the coordinated active site for alkyne-azide click catalysis. ArPolyclickase showcases high efficiency, substrate generality, regioselectivity, and ease of product separation for "click chemistry" in water. Notably, ArPolyclickase displays good biocompatibility without imposing copper toxicity on living cells, which offers the prospect for the upcoming bioorthogonal chemistry.
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Affiliation(s)
- Ningning Zhang
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany.,Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Patrick Bessel
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.,Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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7
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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8
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Xu G, Poelarends GJ. Unlocking New Reactivities in Enzymes by Iminium Catalysis. Angew Chem Int Ed Engl 2022; 61:e202203613. [PMID: 35524737 PMCID: PMC9400869 DOI: 10.1002/anie.202203613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 12/11/2022]
Abstract
The application of biocatalysis in conquering challenging synthesis requires the constant input of new enzymes. Developing novel biocatalysts by absorbing catalysis modes from synthetic chemistry has yielded fruitful new-to-nature enzymes. Organocatalysis was originally bio-inspired and has become the third pillar of asymmetric catalysis. Transferring organocatalytic reactions back to enzyme platforms is a promising approach for biocatalyst creation. Herein, we summarize recent developments in the design of novel biocatalysts that adopt iminium catalysis, a fundamental branch in organocatalysis. By repurposing existing enzymes or constructing artificial enzymes, various biocatalysts for iminium catalysis have been created and optimized via protein engineering to promote valuable abiological transformations. Recent advances in iminium biocatalysis illustrate the power of combining chemomimetic biocatalyst design and directed evolution to generate useful new-to-nature enzymes.
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Affiliation(s)
- Guangcai Xu
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713, AV Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713, AV Groningen, The Netherlands
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9
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Jung SM, Yang M, Song WJ. Symmetry-Adapted Synthesis of Dicopper Oxidases with Divergent Dioxygen Reactivity. Inorg Chem 2022; 61:12433-12441. [DOI: 10.1021/acs.inorgchem.2c01898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Se-Min Jung
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Minwoo Yang
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
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10
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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11
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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12
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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13
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Maity B, Taher M, Mazumdar S, Ueno T. Artificial metalloenzymes based on protein assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Xu G, Poelarends GJ. Unlocking New Reactivities in Enzymes by Iminium Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203613] [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)
- Guangcai Xu
- University of Groningen: Rijksuniversiteit Groningen Chemical and Pharmaceutical Biology NETHERLANDS
| | - Gerrit J. Poelarends
- University of Groningen Chemical and Pharmaceutical Biology Antonius Deusinglaan 1 9713 AV Groningen NETHERLANDS
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15
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Leveson-Gower RB, de Boer RM, Roelfes G. Tandem Friedel‐Crafts Alkylation/Enantioselective Protonation by Artificial Enzyme Iminium Catalysis. ChemCatChem 2022; 14:e202101875. [PMID: 35915643 PMCID: PMC9313897 DOI: 10.1002/cctc.202101875] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/21/2022] [Indexed: 11/08/2022]
Abstract
The incorporation of organocatalysts into protein scaffolds holds the promise of overcoming some of the limitations of this powerful catalytic approach. Previously, we showed that incorporation of the non‐canonical amino acid para‐aminophenylalanine into the non‐enzymatic protein scaffold LmrR forms a proficient and enantioselective artificial enzyme (LmrR_pAF) for the Friedel‐Crafts alkylation of indoles with enals. The unnatural aniline side‐chain is directly involved in catalysis, operating via a well‐known organocatalytic iminium‐based mechanism. In this study, we show that LmrR_pAF can enantioselectively form tertiary carbon centres not only during C−C bond formation, but also by enantioselective protonation, delivering a proton to one face of a prochiral enamine intermediate. The importance of various side‐chains in the pocket of LmrR is distinct from the Friedel‐Crafts reaction without enantioselective protonation, and two particularly important residues were probed by exhaustive mutagenesis.
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Affiliation(s)
| | - Ruben M. de Boer
- Rijksuniversiteit Groningen Stratingh Institute for Chemistry Groningen NETHERLANDS
| | - Gerard Roelfes
- Rijksuniversiteit Groningen Stratingh Institute for Chemistry Nijenborgh 4 9747 AG Groningen NETHERLANDS
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16
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Tian R, Li Y, Xu J, Hou C, Luo Q, Liu J. Recent development in the design of artificial enzymes through molecular imprinting technology. J Mater Chem B 2022; 10:6590-6606. [DOI: 10.1039/d2tb00276k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymes, a class of proteins or RNA with high catalytic efficiency and specificity, have inspired generations of scientists to develop enzyme mimics with similar capabilities. Many enzyme mimics have been...
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17
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Cheng G, Wu Q, Jiang C. Synthesis of highly active enzyme-metal nanohybrids and uncovering the design rules. Enzyme Microb Technol 2021; 154:109962. [PMID: 34915246 DOI: 10.1016/j.enzmictec.2021.109962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022]
Abstract
Nanobiohybrid CAL-B/MNPs were synthesized through enzyme in situ reduction of metal ions, including noble and non-noble metals. Lipase CAL-B acted as multifunctional reagents (reducing and supporting agents). The hybrid catalysts were systematically characterized by HRTEM, EDX, MALDI-TOF-MS, and XPS analysis, confirming that highly dispersed 3-5 nm nanoparticles were evenly dispersed on lipase matrix without agglomeration. The mechanism of CAL-B reducing metal ions was investigated, revealing that AGLFFSSKDL in the amino acid sequence of CAL-B from 111 to 128 formed a stable spatial structure through hydrogen bonding, which was the key factor for enzyme in situ reduction of metal ions into highly dispersed nanoparticles.
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Affiliation(s)
- Guilin Cheng
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, PR China
| | - Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, PR China.
| | - Chengjun Jiang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, 310023 Zhejiang, PR China.
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18
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Laureanti JA, Su Q, Shaw WJ. A protein scaffold enables hydrogen evolution for a Ni-bisdiphosphine complex. Dalton Trans 2021; 50:15754-15759. [PMID: 34704584 DOI: 10.1039/d1dt03295j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An artificial metalloenzyme acting as a functional biomimic of hydrogenase enzymes was activated by assembly via covalent attachment of the molecular complex, [Ni(PNglycineP)2]2-, within a structured protein scaffold. Electrocatalytic H2 production was observed from pH 3.0 to 10.0 for the artificial enzyme, while no electrocatalytic activity was observed for similar [Ni(PNP)2]2+ systems.
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Affiliation(s)
- Joseph A Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Qiwen Su
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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19
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Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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20
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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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21
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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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22
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Vong K, Nasibullin I, Tanaka K. Exploring and Adapting the Molecular Selectivity of Artificial Metalloenzymes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kenward Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
| | - Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
| | - Katsunori Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
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23
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Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold. Nat Chem 2021; 13:231-235. [DOI: 10.1038/s41557-020-00628-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
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24
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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: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [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 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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25
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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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26
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Planas-Iglesias J, Marques SM, Pinto GP, Musil M, Stourac J, Damborsky J, Bednar D. Computational design of enzymes for biotechnological applications. Biotechnol Adv 2021; 47:107696. [PMID: 33513434 DOI: 10.1016/j.biotechadv.2021.107696] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their natural effectiveness has been fine-tuned as a result of millions of years of natural evolution. Such catalytic effectiveness has prompted the use of biocatalysts from multiple sources on different applications, including the industrial production of goods (food and beverages, detergents, textile, and pharmaceutics), environmental protection, and biomedical applications. Natural enzymes often need to be improved by protein engineering to optimize their function in non-native environments. Recent technological advances have greatly facilitated this process by providing the experimental approaches of directed evolution or by enabling computer-assisted applications. Directed evolution mimics the natural selection process in a highly accelerated fashion at the expense of arduous laboratory work and economic resources. Theoretical methods provide predictions and represent an attractive complement to such experiments by waiving their inherent costs. Computational techniques can be used to engineer enzymatic reactivity, substrate specificity and ligand binding, access pathways and ligand transport, and global properties like protein stability, solubility, and flexibility. Theoretical approaches can also identify hotspots on the protein sequence for mutagenesis and predict suitable alternatives for selected positions with expected outcomes. This review covers the latest advances in computational methods for enzyme engineering and presents many successful case studies.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic; IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
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27
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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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28
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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29
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Mejías SH, Roelfes G, Browne WR. Impact of binding to the multidrug resistance regulator protein LmrR on the photo-physics and -chemistry of photosensitizers. Phys Chem Chem Phys 2020; 22:12228-12238. [PMID: 32432253 DOI: 10.1039/d0cp01755h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Light activated photosensitizers generate reactive oxygen species (ROS) that interfere with cellular components and can induce cell death, e.g., in photodynamic therapy (PDT). The effect of cellular components and especially proteins on the photochemistry and photophysics of the sensitizers is a key aspect in drug design and the correlating cellular response with the generation of specific ROS species. Here, we show the complex range of effects of binding of photosensitizer to a multidrug resistance protein, produced by bacteria, on the formers reactivity. We show that recruitment of drug like molecules by LmrR (Lactococcal multidrug resistance Regulator) modifies their photophysical properties and their capacity to induce oxidative stress especially in 1O2 generation, including rose bengal (RB), protoporphyrin IX (PpIX), bodipy, eosin Y (EY), riboflavin (RBF), and rhodamine 6G (Rh6G). The range of neutral and charged dyes with different exited redox potentials, are broadly representative of the dyes used in PDT.
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Affiliation(s)
- Sara H Mejías
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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30
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Ghattas W, Mahy JP, Réglier M, Simaan AJ. Artificial Enzymes for Diels-Alder Reactions. Chembiochem 2020; 22:443-459. [PMID: 32852088 DOI: 10.1002/cbic.202000316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/17/2020] [Indexed: 12/13/2022]
Abstract
The Diels-Alder (DA) reaction is a cycloaddition of a conjugated diene and an alkene (dienophile) leading to the formation of a cyclohexene derivative through a concerted mechanism. As DA reactions generally proceed with a high degree of regio- and stereoselectivity, they are widely used in synthetic organic chemistry. Considering eco-conscious public and governmental movements, efforts are now directed towards the development of synthetic processes that meet environmental concerns. Artificial enzymes, which can be developed to catalyze abiotic reactions, appear to be important synthetic tools in the synthetic biology field. This review describes the different strategies used to develop protein-based artificial enzymes for DA reactions, including for in cellulo approaches.
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Affiliation(s)
- Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, 91405 Cedex 8, France
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, 91405 Cedex 8, France
| | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Avenue Escadrille Normandie Niemen, Service 342, Marseille, 13397, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Avenue Escadrille Normandie Niemen, Service 342, Marseille, 13397, France
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31
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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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32
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Mirzaei Garakani T, Sauer DF, Mertens MAS, Lazar J, Gehrmann J, Arlt M, Schiffels J, Schnakenberg U, Okuda J, Schwaneberg U. FhuA–Grubbs–Hoveyda Biohybrid Catalyst Embedded in a Polymer Film Enables Catalysis in Neat Substrates. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Daniel F. Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | | | - Jaroslav Lazar
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstr. 24, 52074 Aachen, Germany
| | - Julia Gehrmann
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Marcus Arlt
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Johannes Schiffels
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Uwe Schnakenberg
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstr. 24, 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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Himiyama T, Okamoto Y. Artificial Metalloenzymes: From Selective Chemical Transformations to Biochemical Applications. Molecules 2020; 25:molecules25132989. [PMID: 32629938 PMCID: PMC7411666 DOI: 10.3390/molecules25132989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 11/16/2022] Open
Abstract
Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: 1) the newly reported ArMs, according to their type of reaction, and 2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/in vivo catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan;
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Osaka 563-8577, Japan
| | - Yasunori Okamoto
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan
- Correspondence: ; Tel.: +81-22-795-5264
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Liu H, Cao M, Wang Y, Lv B, Li C. Bioengineering oligomerization and monomerization of enzymes: learning from natural evolution to matching the demands for industrial applications. Crit Rev Biotechnol 2020; 40:231-246. [PMID: 31914816 DOI: 10.1080/07388551.2019.1711014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
It is generally accepted that oligomeric enzymes evolve from their monomeric ancestors, and the evolution process generates superior structural benefits for functional advantages. Furthermore, adjusting the transition between different oligomeric states is an important mechanism for natural enzymes to regulate their catalytic functions for adapting environmental fluctuations in nature, which inspires researchers to mimic such a strategy to develop artificially oligomerized enzymes through protein engineering for improved performance under specific conditions. On the other hand, transforming oligomeric enzymes into their monomers is needed in fundamental research for deciphering catalytic mechanisms as well as exploring their catalytic capacities for better industrial applications. In this article, strategies for developing artificially oligomerized and monomerized enzymes are reviewed and highlighted by their applications. Furthermore, advances in the computational prediction of oligomeric structures are introduced, which would accelerate the systematic design of oligomeric and monomeric enzymes. Finally, the current challenges and future directions in this field are discussed.
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Affiliation(s)
- Hu Liu
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Mingming Cao
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ying Wang
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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35
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Alonso S, Santiago G, Cea-Rama I, Fernandez-Lopez L, Coscolín C, Modregger J, Ressmann AK, Martínez-Martínez M, Marrero H, Bargiela R, Pita M, Gonzalez-Alfonso JL, Briand ML, Rojo D, Barbas C, Plou FJ, Golyshin PN, Shahgaldian P, Sanz-Aparicio J, Guallar V, Ferrer M. Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis. Nat Catal 2019. [DOI: 10.1038/s41929-019-0394-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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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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37
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Matsuo T, Miyake T, Hirota S. Recent developments on creation of artificial metalloenzymes. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.151226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Atroposelective antibodies as a designed protein scaffold for artificial metalloenzymes. Sci Rep 2019; 9:13551. [PMID: 31537832 PMCID: PMC6753118 DOI: 10.1038/s41598-019-49844-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/02/2019] [Indexed: 11/09/2022] Open
Abstract
Design and engineering of protein scaffolds are crucial to create artificial metalloenzymes. Herein we report the first example of C-C bond formation catalyzed by artificial metalloenzymes, which consist of monoclonal antibodies (mAbs) and C2 symmetric metal catalysts. Prepared as a tailored protein scaffold for a binaphthyl derivative (BN), mAbs bind metal catalysts bearing a 1,1'-bi-isoquinoline (BIQ) ligand to yield artificial metalloenzymes. These artificial metalloenzymes catalyze the Friedel-Crafts alkylation reaction. In the presence of mAb R44E1, the reaction proceeds with 88% ee. The reaction catalyzed by Cu-catalyst incorporated into the binding site of mAb R44E1 is found to show excellent enantioselectivity with 99% ee. The protein environment also enables the use of BIQ-based catalysts as asymmetric catalysts for the first time.
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40
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Mansot J, Vasseur J, Arseniyadis S, Smietana M. α,β‐Unsaturated 2‐Acyl‐Imidazoles in Asymmetric Biohybrid Catalysis. ChemCatChem 2019. [DOI: 10.1002/cctc.201900743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Justine Mansot
- Institut des Biomolécules Max MousseronUMR 5247 CNRS Université de Montpellier, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Jean‐Jacques Vasseur
- Institut des Biomolécules Max MousseronUMR 5247 CNRS Université de Montpellier, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Stellios Arseniyadis
- Queen Mary University of LondonSchool of Biological and Chemical Sciences Mile End Road E1 4NS London UK
| | - Michael Smietana
- Institut des Biomolécules Max MousseronUMR 5247 CNRS Université de Montpellier, ENSCM Place Eugène Bataillon 34095 Montpellier France
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41
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Rittle J, Field MJ, Green MT, Tezcan FA. An efficient, step-economical strategy for the design of functional metalloproteins. Nat Chem 2019; 11:434-441. [PMID: 30778140 PMCID: PMC6483823 DOI: 10.1038/s41557-019-0218-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/11/2019] [Indexed: 01/31/2023]
Abstract
The bottom-up design and construction of functional metalloproteins remains a formidable task in biomolecular design. Although numerous strategies have been used to create new metalloproteins, pre-existing knowledge of the tertiary and quaternary protein structure is often required to generate suitable platforms for robust metal coordination and activity. Here we report an alternative and easily implemented approach (metal active sites by covalent tethering or MASCoT) in which folded protein building blocks are linked by a single disulfide bond to create diverse metal coordination environments within evolutionarily naive protein-protein interfaces. Metalloproteins generated using this strategy uniformly bind a wide array of first-row transition metal ions (MnII, FeII, CoII, NiII, CuII, ZnII and vanadyl) with physiologically relevant thermodynamic affinities (dissociation constants ranging from 700 nM for MnII to 50 fM for CuII). MASCoT readily affords coordinatively unsaturated metal centres-including a penta-His-coordinated non-haem Fe site-and well-defined binding pockets that can accommodate modifications and enable coordination of exogenous ligands such as nitric oxide to the interfacial metal centre.
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Affiliation(s)
- Jonathan Rittle
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Mackenzie J Field
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Michael T Green
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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42
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Alonso-Cotchico L, Rodríguez-Guerra Pedregal J, Lledós A, Maréchal JD. The Effect of Cofactor Binding on the Conformational Plasticity of the Biological Receptors in Artificial Metalloenzymes: The Case Study of LmrR. Front Chem 2019; 7:211. [PMID: 31024897 PMCID: PMC6467942 DOI: 10.3389/fchem.2019.00211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/18/2019] [Indexed: 12/21/2022] Open
Abstract
The design of Artificial Metalloenzymes (ArMs), which result from the incorporation of organometallic cofactors into biological structures, has grown steadily in the last two decades and important new-to-Nature reactions have been reached. These type of exercises could greatly benefit from an understanding of the structural impact that the inclusion of organometallic moieties may have on the biological host. To date though, our understanding of this phenomenon is highly partial. This lack of knowledge is one of the elements that condition that first-generation ArMs generally display relatively poor catalytic profiles. In this work, we approach this matter by assessing the dynamics and stability of a series of ArMs resulting from the inclusion, via different anchoring strategies, of a variety of organometallic cofactors into the Lactococcal multidrug resistance regulator (LmrR) protein. To this aim, we coupled standard force field-based techniques such as Protein-Ligand Docking and Molecular Dynamics simulations with a variety of trajectory convergence analyses, capable of assessing both the stability and flexibility of the different systems under study upon the binding of cofactors. Together with the experimental evidence obtained in other studies, we provide an overview on how these changes can affect the catalytic outcomes obtained from the different ArMs. Fundamentally, our results show that the convergence analysis used in this work can assess how the inclusion of synthetic metallic cofactors in proteins can condition different structural modulations of their host. Those conformational modifications are key to the success of the desired catalytic activity and their proper identification can be wisely used to improve the quality and the rate of success of the ArMs.
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Affiliation(s)
- Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.,Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | | | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
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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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44
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Lichman BR, O'Connor SE, Kries H. Biocatalytic Strategies towards [4+2] Cycloadditions. Chemistry 2019; 25:6864-6877. [DOI: 10.1002/chem.201805412] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Benjamin R. Lichman
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
- Current address: Department of Biology; University of York; York YO10 5YW UK
| | - Sarah E. O'Connor
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
| | - Hajo Kries
- Independent Junior Research Group, Biosynthetic Design of Natural Products; Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena); Beutenbergstr. 11a 07745 Jena Germany
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45
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Wang Y, Astruc D, Abd-El-Aziz AS. Metallopolymers for advanced sustainable applications. Chem Soc Rev 2019; 48:558-636. [PMID: 30506080 DOI: 10.1039/c7cs00656j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Since the development of metallopolymers, there has been tremendous interest in the applications of this type of materials. The interest in these materials stems from their potential use in industry as catalysts, biomedical agents in healthcare, energy storage and production as well as climate change mitigation. The past two decades have clearly shown exponential growth in the development of many new classes of metallopolymers that address these issues. Today, metallopolymers are considered to be at the forefront for discovering new and sustainable heterogeneous catalysts, therapeutics for drug-resistant diseases, energy storage and photovoltaics, molecular barometers and thermometers, as well as carbon dioxide sequesters. The focus of this review is to highlight the advances in design of metallopolymers with specific sustainable applications.
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Affiliation(s)
- Yanlan Wang
- Liaocheng University, Department of Chemistry and Chemical Engineering, 252059, Liaocheng, China.
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46
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Clarke DE, Noguchi H, Gryspeerdt JLAG, De Feyter S, Voet ARD. Artificial β-propeller protein-based hydrolases. Chem Commun (Camb) 2019; 55:8880-8883. [DOI: 10.1039/c9cc04388h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We investigated symmetrical β-propeller protein scaffolds as artificial hydrolases and discovered their catalytic mechanism to be centred around a threonine–histidine dyad.
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Affiliation(s)
- David E. Clarke
- Division of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- Leuven
- Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | | | - Steven De Feyter
- Division of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- Leuven
- Belgium
| | - Arnout R. D. Voet
- Laboratory of Biomolecular Modelling and Design
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
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47
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Laureanti JA, Buchko GW, Katipamula S, Su Q, Linehan JC, Zadvornyy OA, Peters JW, O’Hagan M. Protein Scaffold Activates Catalytic CO2 Hydrogenation by a Rhodium Bis(diphosphine) Complex. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02615] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Joseph A. Laureanti
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Sriram Katipamula
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Qiwen Su
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - John C. Linehan
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Molly O’Hagan
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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48
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Keller SG, Pannwitz A, Schwizer F, Klehr J, Wenger OS, Ward TR. Light-driven electron injection from a biotinylated triarylamine donor to [Ru(diimine)3](2+)-labeled streptavidin. Org Biomol Chem 2018; 14:7197-201. [PMID: 27411288 DOI: 10.1039/c6ob01273f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Electron transfer from a biotinylated electron donor to photochemically generated Ru(iii) complexes covalently anchored to streptavidin is demonstrated by means of time-resolved laser spectroscopy. Through site-selective mutagenesis, a single cysteine residue was engineered at four different positions on streptavidin, and a Ru(ii) tris-diimine complex was then bioconjugated to the exposed cysteines. A biotinylated triarylamine electron donor was added to the Ru(ii)-modified streptavidins to afford dyads localized within a streptavidin host. The resulting systems were subjected to electron transfer studies. In some of the explored mutants, the phototriggered electron transfer between triarylamine and Ru(iii) is complete within 10 ns, thus highlighting the potential of such artificial metalloenzymes to perform photoredox catalysis.
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Affiliation(s)
- Sascha G Keller
- Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland.
| | - Andrea Pannwitz
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland.
| | - Fabian Schwizer
- Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland.
| | - Juliane Klehr
- Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland.
| | - Oliver S Wenger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland.
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland.
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49
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Almhjell PJ, Mills JH. Metal-chelating non-canonical amino acids in metalloprotein engineering and design. Curr Opin Struct Biol 2018; 51:170-176. [DOI: 10.1016/j.sbi.2018.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/12/2018] [Indexed: 11/26/2022]
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50
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A designer enzyme for hydrazone and oxime formation featuring an unnatural catalytic aniline residue. Nat Chem 2018; 10:946-952. [PMID: 29967395 DOI: 10.1038/s41557-018-0082-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 05/15/2018] [Indexed: 11/08/2022]
Abstract
Creating designer enzymes with the ability to catalyse abiological transformations is a formidable challenge. Efforts toward this goal typically consider only canonical amino acids in the initial design process. However, incorporating unnatural amino acids that feature uniquely reactive side chains could significantly expand the catalytic repertoire of designer enzymes. To explore the potential of such artificial building blocks for enzyme design, here we selected p-aminophenylalanine as a potentially novel catalytic residue. We demonstrate that the catalytic activity of the aniline side chain for hydrazone and oxime formation reactions is increased by embedding p-aminophenylalanine into the hydrophobic pore of the multidrug transcriptional regulator from Lactococcus lactis. Both the recruitment of reactants by the promiscuous binding pocket and a judiciously placed aniline that functions as a catalytic residue contribute to the success of the identified artificial enzyme. We anticipate that our design strategy will prove rewarding to significantly expand the catalytic repertoire of designer enzymes in the future.
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