1
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Vargiu M, Xu Y, Kuipers OP, Roelfes G. Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides. Chembiochem 2024; 25:e202400043. [PMID: 38334959 DOI: 10.1002/cbic.202400043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity remained good, albeit lower than the unmodified peptide. Also the lanthipeptide nisin could be modified using this method.
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Affiliation(s)
- Michela Vargiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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2
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Ofori Atta L, Zhou Z, Roelfes G. In Vivo Biocatalytic Cascades Featuring an Artificial-Enzyme-Catalysed New-to-Nature Reaction. Angew Chem Int Ed Engl 2023; 62:e202214191. [PMID: 36342952 PMCID: PMC10100225 DOI: 10.1002/anie.202214191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Indexed: 11/09/2022]
Abstract
Artificial enzymes utilizing the genetically encoded non-proteinogenic amino acid p-aminophenylalanine (pAF) as a catalytic residue are able to react with carbonyl compounds through an iminium ion mechanism to promote reactions that have no equivalent in nature. Herein, we report an in vivo biocatalytic cascade that is augmented with such an artificial enzyme-catalysed new-to-nature reaction. The artificial enzyme in this study is a pAF-containing evolved variant of the lactococcal multidrug-resistance regulator, designated LmrR_V15pAF_RMH, which efficiently converts benzaldehyde derivatives produced in vivo into the corresponding hydrazone products inside E. coli cells. These in vivo biocatalytic cascades comprising an artificial-enzyme-catalysed reaction are an important step towards achieving a hybrid metabolism.
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Affiliation(s)
- Linda Ofori Atta
- 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.,Current address: School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
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3
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Atta LO, Zhou Z, Roelfes G. In vivo Biocatalytic Cascades Featuring an Artificial‐Enzyme‐Catalyzed New‐to‐Nature Reaction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Linda Ofori Atta
- Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Zhi Zhou
- Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Gerard Roelfes
- Rijksuniversiteit Groningen Stratingh Institute for Chemistry Nijenborgh 4 9747 AG Groningen NETHERLANDS
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4
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Zhou Z, Roelfes G. Synergistic Catalysis of Tandem Michael Addition/Enantioselective Protonation Reactions by an Artificial Enzyme. ACS Catal 2021; 11:9366-9369. [PMID: 34386272 PMCID: PMC8353628 DOI: 10.1021/acscatal.1c02298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/28/2021] [Indexed: 12/16/2022]
Abstract
Enantioselective protonation is conceptually one of the most attractive methods to generate an α-chiral center. However, enantioselective protonation presents major challenges, especially in water. Herein, we report a tandem Michael addition/enantioselective protonation reaction catalyzed by an artificial enzyme employing two abiological catalytic sites in a synergistic fashion: a genetically encoded noncanonical p-aminophenylalanine residue and a Lewis acid Cu(II) complex. The exquisite stereocontrol achieved in the protonation of the transient enamine intermediate is illustrated by up to >20:1 dr and >99% ee of the product. These results illustrate the potential of exploiting synergistic catalysis in artificial enzymes for challenging reactions.
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Affiliation(s)
- Zhi Zhou
- 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
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7
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Roelfes G. Repurposed and artificial heme enzymes for cyclopropanation reactions. J Inorg Biochem 2021; 222:111523. [PMID: 34217039 DOI: 10.1016/j.jinorgbio.2021.111523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
Heme enzymes are some of the most versatile catalysts in nature. In recent years it has been found that they can also catalyze reactions for which there are no equivalents in nature. This development has been driven by the abiological catalytic reactivity reported for bio-inspired and biomimetic iron porphyrin complexes. This review focuss es on heme enzymes for catalysis of cyclopropanation reactions. The two most important approaches used to create enzymes for cyclopropanation are repurposing of heme enzymes and the various strategies used to improve these enzymes such as mutagenesis and heme replacement, and artificial heme enzymes. These strategies are introduced and compared. Moreover, lessons learned with regard to mechanism and design principles are discussed.
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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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Iyer A, Baranov M, Foster AJ, Chordia S, Roelfes G, Vlijm R, van den Bogaart G, Poolman B. Chemogenetic Tags with Probe Exchange for Live-Cell Fluorescence Microscopy. ACS Chem Biol 2021; 16:891-904. [PMID: 33913682 PMCID: PMC8154248 DOI: 10.1021/acschembio.1c00100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022]
Abstract
Fluorogenic protein tagging systems have been less developed for prokaryotes than for eukaryotic cell systems. Here, we extend the concept of noncovalent fluorogenic protein tags in bacteria by introducing transcription factor-based tags, namely, LmrR and RamR, for probe binding and fluorescence readout under aerobic and anaerobic conditions. We developed two chemogenetic protein tags that impart fluorogenicity and a longer fluorescence lifetime to reversibly bound organic fluorophores, hence the name Chemogenetic Tags with Probe Exchange (CTPEs). We present an extensive characterization of 30 fluorophores reversibly interacting with the two different CTPEs and conclude that aromatic planar structures bind with high specificity to the hydrophobic pockets of these tags. The reversible binding of organic fluorophores to the CTPEs and the superior photophysical properties of organic fluorophores enable long-term fluorescence microscopy of living bacterial cells. Our protein tags provide a general tool for investigating (sub)cellular protein localization and dynamics, protein-protein interactions, and prolonged live-cell microscopy, even under oxygen-free conditions.
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Affiliation(s)
- Aditya Iyer
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maxim Baranov
- Department
of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Alexander J. Foster
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, 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
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Rifka Vlijm
- Molecular
Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Geert van den Bogaart
- Department
of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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10
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de Vries RH, Viel JH, Kuipers OP, Roelfes G. Rapid and Selective Chemical Editing of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) via Cu II -Catalyzed β-Borylation of Dehydroamino Acids. Angew Chem Int Ed Engl 2021; 60:3946-3950. [PMID: 33185967 PMCID: PMC7898795 DOI: 10.1002/anie.202011460] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 12/22/2022]
Abstract
We report the fast and selective chemical editing of ribosomally synthesized and post-translationally modified peptides (RiPPs) by β-borylation of dehydroalanine (Dha) residues. The thiopeptide thiostrepton was modified efficiently using CuII -catalysis under mild conditions and 1D/2D NMR of the purified product showed site-selective borylation of the terminal Dha residues. Using similar conditions, the thiopeptide nosiheptide, lanthipeptide nisin Z, and protein SUMO_G98Dha were also modified efficiently. Borylated thiostrepton showed an up to 84-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity was maintained in thiostrepton and nosiheptide. The introduced boronic-acid functionalities were shown to be valuable handles for chemical mutagenesis and in a reversible click reaction with triols for the pH-controlled labeling of RiPPs.
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Affiliation(s)
- Reinder H. de Vries
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jakob H. Viel
- Department of Molecular GeneticsGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Oscar P. Kuipers
- Department of Molecular GeneticsGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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11
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Affiliation(s)
- Ruben V. Maaskant
- 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
| | - Gerard Roelfes
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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12
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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: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Vries RH, Viel JH, Kuipers OP, Roelfes G. Rapid and Selective Chemical Editing of Ribosomally Synthesized and Post‐Translationally Modified Peptides (RiPPs) via Cu
II
‐Catalyzed β‐Borylation of Dehydroamino Acids. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Reinder H. Vries
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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15
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van Lier RCW, de Bruijn AD, Roelfes G. A Water-Soluble Iridium Photocatalyst for Chemical Modification of Dehydroalanines in Peptides and Proteins. Chemistry 2020; 27:1430-1437. [PMID: 32896943 PMCID: PMC7898865 DOI: 10.1002/chem.202002599] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/04/2020] [Indexed: 12/27/2022]
Abstract
Dehydroalanine (Dha) residues are attractive noncanonical amino acids that occur naturally in ribosomally synthesised and post-translationally modified peptides (RiPPs). Dha residues are attractive targets for selective late-stage modification of these complex biomolecules. In this work, we show the selective photocatalytic modification of dehydroalanine residues in the antimicrobial peptide nisin and in the proteins small ubiquitin-like modifier (SUMO) and superfolder green fluorescent protein (sfGFP). For this purpose, a new water-soluble iridium(III) photoredox catalyst was used. The design and synthesis of this new photocatalyst, [Ir(dF(CF3 )ppy)2 (dNMe3 bpy)]Cl3 , is presented. In contrast to commonly used iridium photocatalysts, this complex is highly water soluble and allows peptides and proteins to be modified in water and aqueous solvents under physiologically relevant conditions, with short reaction times and with low reagent and catalyst loadings. This work suggests that photoredox catalysis using this newly designed catalyst is a promising strategy to modify dehydroalanine-containing natural products and thus could have great potential for novel bioconjugation strategies.
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Affiliation(s)
- Roos C W van Lier
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - A Dowine de Bruijn
- 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
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Drienovská I, Scheele RA, Gutiérrez de Souza C, Roelfes G. A Hydroxyquinoline-Based Unnatural Amino Acid for the Design of Novel Artificial Metalloenzymes. Chembiochem 2020; 21:3077-3081. [PMID: 32585070 PMCID: PMC7689906 DOI: 10.1002/cbic.202000306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Indexed: 11/11/2022]
Abstract
We have examined the potential of the noncanonical amino acid (8-hydroxyquinolin-3-yl)alanine (HQAla) for the design of artificial metalloenzymes. HQAla, a versatile chelator of late transition metals, was introduced into the lactococcal multidrug-resistance regulator (LmrR) by stop codon suppression methodology. LmrR_HQAla was shown to complex efficiently with three different metal ions, CuII , ZnII and RhIII to form unique artificial metalloenzymes. The catalytic potential of the CuII -bound LmrR_HQAla enzyme was shown through its ability to catalyse asymmetric Friedel-Craft alkylation and water addition, whereas the ZnII -coupled enzyme was shown to mimic natural Zn hydrolase activity.
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Affiliation(s)
- Ivana Drienovská
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Remkes A. Scheele
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Cora Gutiérrez de Souza
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Abstract
We report the efficient and selective Cu(ii)-catalysed β-silylation of naturally occurring dehydroalanine (Dha) residues in various ribosomally synthesized and post-translationally modified peptides (RiPPs). The method is also applicable to proteins, as was shown by the modification of a Dha residue that was chemically introduced into Small Ubiquitin-like Modifier (SUMO).
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Affiliation(s)
- Reinder H de Vries
- 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.
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20
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Li Z, Chakraborty P, de Vries RH, Song C, Zhao X, Roelfes G, Scheffers DJ, Kuipers OP. Characterization of two relacidines belonging to a novel class of circular lipopeptides that act against Gram-negative bacterial pathogens. Environ Microbiol 2020; 22:5125-5136. [PMID: 32608161 PMCID: PMC7818431 DOI: 10.1111/1462-2920.15145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022]
Abstract
The development of sustainable agriculture and the increasing antibiotic resistance of human pathogens call for novel antimicrobial compounds. Here, we describe the extraction and characterization of a class of cationic circular lipopeptides, for which we propose the name relacidines, from the soil bacterium Brevibacillus laterosporus MG64. Relacidines are composed of a fatty acid side chain (4‐methylhexanoic acid) and 13 amino acid residues. A lactone ring is formed by the last five amino acid residues and three positively charged ornithines are located in the linear fragment. Relacidines selectively combat Gram‐negative pathogens, including phytopathogens and human pathogens. Further investigation of the mode of action revealed that relacidine B binds to the lipopolysaccharides but does not form pores in the cell membrane. We also provide proof to show that relacidine B does not affect the biosynthesis of the cell wall and RNA. Instead, it affects the oxidative phosphorylation process of cells and diminishes the biosynthesis of ATP. Transcription of relacidines is induced by plant pathogens, which strengthens the potential of B. laterosporus MG64 to be used as a biocontrol agent. Thus, we identified a new group of potent antibiotic compounds for combating Gram‐negative pathogens of plants or animals.
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Affiliation(s)
- Zhibo Li
- Department of Molecular Genetics, University of Groningen, Groningen, the Netherlands
| | - Parichita Chakraborty
- Department of Molecular Microbiology, University of Groningen, Groningen, the Netherlands
| | - Reinder H de Vries
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Chunxu Song
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interaction, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Xinghong Zhao
- Department of Molecular Genetics, University of Groningen, Groningen, the Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Dirk-Jan Scheffers
- Department of Molecular Microbiology, University of Groningen, Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, the Netherlands
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21
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Gutiérrez de Souza C, Bersellini M, Roelfes G. Artificial Metalloenzymes based on TetR Proteins and Cu(II) for Enantioselective Friedel-Crafts Alkylation Reactions. ChemCatChem 2020; 12:3190-3194. [PMID: 32612714 PMCID: PMC7319431 DOI: 10.1002/cctc.202000245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/31/2020] [Indexed: 12/16/2022]
Abstract
The supramolecular approach is among the most convenient methodologies for creating artificial metalloenzymes (ArMs). Usually this approach involves the binding of a transition metal ion complex to a biomolecular scaffold via its ligand, which also modulates the catalytic properties of the metal ion. Herein, we report ArMs based on the proteins CgmR, RamR and QacR from the TetR family of multidrug resistance regulators (MDRs) and Cu2+ ions, assembled without the need of a ligand. These ArMs catalyze the enantioselective vinylogous Friedel-Crafts alkylation reaction with up to 75 % ee. Competition experiments with ethidium and rhodamine 6G confirm that the reactions occur in the chiral environment of the hydrophobic pocket. It is proposed that the Cu2+-substrate complex is bound via a combination of electrostatic and π-stacking interactions provided by the second coordination sphere. This approach constitutes a fast and straightforward way to assemble metalloenzymes and may facilitate future optimization of the protein scaffolds via mutagenesis or directed evolution approaches.
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Affiliation(s)
- Cora Gutiérrez de Souza
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh49747AG GroningenThe Netherlands
| | - Manuela Bersellini
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh49747AG GroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh49747AG GroningenThe Netherlands
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22
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Syga Ł, de Vries RH, van Oosterhout H, Bartelds R, Boersma AJ, Roelfes G, Poolman B. A Trifunctional Linker for Palmitoylation and Peptide and Protein Localization in Biological Membranes. Chembiochem 2020; 21:1320-1328. [PMID: 31814256 PMCID: PMC7317724 DOI: 10.1002/cbic.201900655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 01/09/2023]
Abstract
Attachment of lipophilic groups is an important post-translational modification of proteins, which involves the coupling of one or more anchors such as fatty acids, isoprenoids, phospholipids, or glycosylphosphatidyl inositols. To study its impact on the membrane partitioning of hydrophobic peptides or proteins, we designed a tyrosine-based trifunctional linker. The linker allows the facile incorporation of two different functionalities at a cysteine residue in a single step. We determined the effect of the lipid modification on the membrane partitioning of the synthetic α-helical model peptide WALP with or without here and in all cases below; palmitoyl groups in giant unilamellar vesicles that contain a liquid-ordered (Lo ) and liquid-disordered (Ld ) phase. Introduction of two palmitoyl groups did not alter the localization of the membrane peptides, nor did the membrane thickness or lipid composition. In all cases, the peptide was retained in the Ld phase. These data demonstrate that the Lo domain in model membranes is highly unfavorable for a single membrane-spanning peptide.
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Affiliation(s)
- Łukasz Syga
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Reinder H. de Vries
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Hugo van Oosterhout
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Rianne Bartelds
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Arnold J. Boersma
- DWI Leibniz Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| | - Gerard Roelfes
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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23
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Syga Ł, Vries RH, Oosterhout H, Bartelds R, Boersma AJ, Roelfes G, Poolman B. Cover Feature: A Trifunctional Linker for Palmitoylation and Peptide and Protein Localization in Biological Membranes (ChemBioChem 9/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Łukasz Syga
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Reinder H. Vries
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Hugo Oosterhout
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Rianne Bartelds
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Arnold J. Boersma
- DWI Leibniz Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | - Gerard Roelfes
- Department of Biomolecular Chemistry and CatalysisStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Sciences andBiotechnology Institute and Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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24
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25
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Maaskant RV, Polanco EA, van Lier RCW, Roelfes G. Cationic iron porphyrins with sodium dodecyl sulphate for micellar catalysis of cyclopropanation reactions. Org Biomol Chem 2020; 18:638-641. [DOI: 10.1039/c9ob02223f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we report that the combination of cationic iron porphyrins with sodium dodecyl sulphate (SDS) gives rise to efficient micellar catalysis of cyclopropanation reactions of styrene derivatives, using diazoacetates as carbene precursors.
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Affiliation(s)
- Ruben V. Maaskant
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Ehider A. Polanco
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Roos C. W. van Lier
- 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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26
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27
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de Vries RH, Viel JH, Oudshoorn R, Kuipers OP, Roelfes G. Selective Modification of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) through Diels-Alder Cycloadditions on Dehydroalanine Residues. Chemistry 2019; 25:12698-12702. [PMID: 31361053 PMCID: PMC6790694 DOI: 10.1002/chem.201902907] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Indexed: 11/08/2022]
Abstract
We report the late‐stage chemical modification of ribosomally synthesized and post‐translationally modified peptides (RIPPs) by Diels–Alder cycloadditions to naturally occurring dehydroalanines. The tail region of the thiopeptide thiostrepton could be modified selectively and efficiently under microwave heating and transition‐metal‐free conditions. The Diels–Alder adducts were isolated and the different site‐ and endo/exo isomers were identified by 1D/2D 1H NMR. Via efficient modification of the thiopeptide nosiheptide and the lanthipeptide nisin Z the generality of the method was established. Minimum inhibitory concentration (MIC) assays of the purified thiostrepton Diels–Alder products against thiostrepton‐susceptible strains displayed high activities comparable to that of native thiostrepton. These Diels–Alder products were also subjected successfully to inverse‐electron‐demand Diels–Alder reactions with a variety of functionalized tetrazines, demonstrating the utility of this method for labeling of RiPPs.
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Affiliation(s)
- Reinder H de Vries
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Jakob H Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Ruben Oudshoorn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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28
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Geersing A, de Vries RH, Jansen G, Rots MG, Roelfes G. Folic acid conjugates of a bleomycin mimic for selective targeting of folate receptor positive cancer cells. Bioorg Med Chem Lett 2019; 29:1922-1927. [DOI: 10.1016/j.bmcl.2019.05.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 10/26/2022]
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Alonso-Cotchico L, Sciortino G, Vidossich P, Rodríguez-Guerra Pedregal J, Drienovská I, Roelfes G, Lledós A, Maréchal JD. Integrated Computational Study of the Cu-Catalyzed Hydration of Alkenes in Water Solvent and into the Context of an Artificial Metallohydratase. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Pietro Vidossich
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
- COBO Computational Bio-Organic Chemistry Bogotá, Department of Chemistry, Universidad de los Andes, Carrera 1 N° 18A 10, Bogotá 111711, Colombia
| | | | - Ivana Drienovská
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Agusti Lledós
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, 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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31
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Alonso-Cotchico L, Roelfes G. A "Broad Spectrum" Carbene Transferase for Synthesis of Chiral α-Trifluoromethylated Organoborons. ACS Cent Sci 2019; 5:206-208. [PMID: 30834308 PMCID: PMC6396192 DOI: 10.1021/acscentsci.9b00015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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Mayer C, Dulson C, Reddem E, Thunnissen AWH, Roelfes G. Directed Evolution of a Designer Enzyme Featuring an Unnatural Catalytic Amino Acid. Angew Chem Int Ed Engl 2019; 58:2083-2087. [PMID: 30575260 PMCID: PMC6519144 DOI: 10.1002/anie.201813499] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/15/2022]
Abstract
The impressive rate accelerations that enzymes display in nature often result from boosting the inherent catalytic activities of side chains by their precise positioning inside a protein binding pocket. Such fine-tuning is also possible for catalytic unnatural amino acids. Specifically, the directed evolution of a recently described designer enzyme, which utilizes an aniline side chain to promote a model hydrazone formation reaction, is reported. Consecutive rounds of directed evolution identified several mutations in the promiscuous binding pocket, in which the unnatural amino acid is embedded in the starting catalyst. When combined, these mutations boost the turnover frequency (kcat ) of the designer enzyme by almost 100-fold. This results from strengthening the catalytic contribution of the unnatural amino acid, as the engineered designer enzymes outperform variants, in which the aniline side chain is replaced with a catalytically inactive tyrosine residue, by more than 200-fold.
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Affiliation(s)
- Clemens Mayer
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
| | - Christopher Dulson
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
| | - Eswar Reddem
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
| | - Andy‐Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
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33
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Mayer C, Dulson C, Reddem E, Thunnissen AMWH, Roelfes G. Directed Evolution of a Designer Enzyme Featuring an Unnatural Catalytic Amino Acid. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Clemens Mayer
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
| | - Christopher Dulson
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
| | - Eswar Reddem
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 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
| | - Gerard Roelfes
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
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Abstract
Bioorthogonal catalytic modification of ribosomally synthesized and post-translationally modified peptides (RiPPs) is a promising approach to obtaining novel antimicrobial peptides with improved properties and/or activities. Here, we present the serendipitous discovery of a selective and rapid method for the alkylation of methionines in the lanthipeptide nisin. Using carbenes, formed from water-soluble metalloporphyrins and diazoacetates, methionines are alkylated to obtain sulfonium ions. The formed sulfonium ions are stable, but can be further reacted to obtain functionalized methionine analogues, expanding the toolbox of chemical posttranslational modification even further.
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Affiliation(s)
- Ruben V. Maaskant
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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35
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Abstract
Dehydroalanine (Dha) and dehydrobutyrine (Dhb) are remarkably versatile non-canonical amino acids often found in antimicrobial peptides. This work presents the selective modification of Dha and Dhb in antimicrobial peptides through photocatalytic activation of organoborates under the influence of visible light. Ir(dF(CF3 )ppy)2 (dtbbpy)PF6 was used as a photoredox catalyst in aqueous solutions for the modification of thiostrepton and nisin. The mild conditions and high selectivity for the dehydrated residues show that photoredox catalysis is a promising tool for the modification of peptide-derived natural products.
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Affiliation(s)
- A. Dowine de Bruijn
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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36
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van der Velde JHM, Oelerich J, Huang J, Smit JH, Jazi AA, Galiani S, Kolmakov K, Gouridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T. Author Correction: A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nat Commun 2018; 9:16232. [PMID: 30039809 PMCID: PMC6063355 DOI: 10.1038/ncomms16232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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de Bruijn AD, Roelfes G. Catalytic Modification of Dehydroalanine in Peptides and Proteins by Palladium-Mediated Cross-Coupling. Chemistry 2018; 24:12728-12733. [PMID: 29923249 PMCID: PMC6146911 DOI: 10.1002/chem.201802846] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/18/2018] [Indexed: 11/16/2022]
Abstract
Dehydroalanine (Dha) is a remarkably versatile non‐canonical amino acid often found in antimicrobial peptides. Herein, we present the catalytic modification of Dha by a palladium‐mediated cross‐coupling reaction. By using Pd(EDTA)(OAc)2 as water‐soluble catalyst, a variety of arylboronic acids was coupled to the dehydrated residues in proteins and peptides, such as Nisin. The cross‐coupling reaction gave both the Heck product, in which the sp2‐hybridisation of the α‐carbon is retained, as well as the conjugated addition product. The reaction can be performed under mild aqueous conditions, which makes this method an attractive addition to the palette of bio‐orthogonal catalytic methods.
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Affiliation(s)
- A Dowine de Bruijn
- 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
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38
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Geersing A, Ségaud N, van der Wijst MGP, Rots MG, Roelfes G. Importance of Metal-Ion Exchange for the Biological Activity of Coordination Complexes of the Biomimetic Ligand N4Py. Inorg Chem 2018; 57:7748-7756. [PMID: 29916702 PMCID: PMC6030684 DOI: 10.1021/acs.inorgchem.8b00714] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 12/24/2022]
Abstract
Metal coordination complexes can display interesting biological activity, as illustrated by the bleomycins (BLMs), a family of natural antibiotics that when coordinated to a redox-active metal ion, show antitumor activity. Yet, which metal ion is required for the activity in cells is still subject to debate. In this study, we described how different metal ions affect the intracellular behavior and activity of the synthetic BLM-mimic N, N-bis(2-pyridylmethyl)- N-bis(2-pyridyl)methylamine (N4Py). Our study shows that a mixture of iron(II), copper(II), and zinc(II) complexes can be generated when N4Py is added to cell cultures but that the metal ion can also be exchanged by other metal ions present in cells. Moreover, the combination of chemical data, together with the performed biological experiments, shows that the active complex causing oxidative damage to cells is the FeII-N4Py complex and not per se the metal complex that was initially added to the cell culture medium. Finally, it is proposed that the high activity observed upon the addition of the free N4Py ligand is the result of a combination of scavenging of biologically relevant metals and oxidative damage caused by the iron(II) complex.
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Affiliation(s)
- Arjan Geersing
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nathalie Ségaud
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Monique G. P. van der Wijst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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39
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Villarino L, Splan KE, Reddem E, Alonso‐Cotchico L, Gutiérrez de Souza C, Lledós A, Maréchal J, Thunnissen AWH, Roelfes G. An Artificial Heme Enzyme for Cyclopropanation Reactions. Angew Chem Int Ed Engl 2018; 57:7785-7789. [PMID: 29719099 PMCID: PMC6033091 DOI: 10.1002/anie.201802946] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Indexed: 12/12/2022]
Abstract
An artificial heme enzyme was created through self-assembly from hemin and the lactococcal multidrug resistance regulator (LmrR). The crystal structure shows the heme bound inside the hydrophobic pore of the protein, where it appears inaccessible for substrates. However, good catalytic activity and moderate enantioselectivity was observed in an abiological cyclopropanation reaction. We propose that the dynamic nature of the structure of the LmrR protein is key to the observed activity. This was supported by molecular dynamics simulations, which showed transient formation of opened conformations that allow the binding of substrates and the formation of pre-catalytic structures.
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Affiliation(s)
- Lara Villarino
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Kathryn E. Splan
- Department of ChemistryMacalester College1600 Grand AvenueSaint PaulMN55105USA
| | - Eswar Reddem
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Lur Alonso‐Cotchico
- Departament de QuímicaUniversitat Autònoma de BarcelonaEdifici C.n.08193 Cerdanyola del VallésBarcelonaSpain
| | - Cora Gutiérrez de Souza
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Agustí Lledós
- Departament de QuímicaUniversitat Autònoma de BarcelonaEdifici C.n.08193 Cerdanyola del VallésBarcelonaSpain
| | - Jean‐Didier Maréchal
- Departament de QuímicaUniversitat Autònoma de BarcelonaEdifici C.n.08193 Cerdanyola del VallésBarcelonaSpain
| | - Andy‐Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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40
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Villarino L, Splan KE, Reddem E, Alonso-Cotchico L, Gutiérrez de Souza C, Lledós A, Maréchal JD, Thunnissen AMWH, Roelfes G. An Artificial Heme Enzyme for Cyclopropanation Reactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802946] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lara Villarino
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Kathryn E. Splan
- Department of Chemistry; Macalester College; 1600 Grand Avenue Saint Paul MN 55105 USA
| | - Eswar Reddem
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Lur Alonso-Cotchico
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdanyola del Vallés Barcelona Spain
| | - Cora Gutiérrez de Souza
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Agustí Lledós
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdanyola del Vallés Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdanyola del Vallés Barcelona Spain
| | - Andy-Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute; 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
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41
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Abstract
A novel and versatile design of DNA-lipid conjugates is presented. The assembly of the DNA headgroups into G-quadruplex structures is essential for the formation of micelles and their stability. By hybridization with a complementary oligonucleotide the micelles were destabilized, resulting in cargo release. In combination with a hairpin DNA aptamer as complementary strand, the release is obtained selectively by the presence of ATP.
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Affiliation(s)
- Liliana Cozzoli
- Stratingh Institute for Chemistry, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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42
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Abstract
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The interaction of a number of first-row
transition-metal ions with a 2,2′-bipyridyl alanine (bpyA)
unit incorporated into the lactococcal multidrug resistance regulator
(LmrR) scaffold is reported. The composition of the active site is
shown to influence binding affinities. In the case of Fe(II), we demonstrate
the need of additional ligating residues, in particular those containing
carboxylate groups, in the vicinity of the binding site. Moreover,
stabilization of di-tert-butylsemiquinone radical
(DTB-SQ) in water was achieved by binding to the designed
metalloproteins, which resulted in the radical being shielded from
the aqueous environment. This allowed the first characterization of
the radical semiquinone in water by resonance Raman spectroscopy. A coordination study of first-row transition-metal ions to bipyridine
alanine (bpyA) incorporated into the lactococcal multidrug resistance
regulator (LmrR) scaffold is reported. The designed metalloproteins
were shown to bind and stabilize the di-tert-butylsemiquinone
radical (DTB-SQ) in water, allowing for the first resonance
Raman characterization of this radical species in water.
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Affiliation(s)
- Nathalie Ségaud
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Drienovská
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Juan Chen
- 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
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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43
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Drienovská I, Alonso-Cotchico L, Vidossich P, Lledós A, Maréchal JD, Roelfes G. Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid. Chem Sci 2017; 8:7228-7235. [PMID: 29081955 PMCID: PMC5633786 DOI: 10.1039/c7sc03477f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023] Open
Abstract
The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the in vivo incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-defined metal-binding site. Here, we report a designed artificial metallohydratase, based on the transcriptional repressor lactococcal multidrug resistance regulator (LmrR), in which the non-canonical amino acid (2,2'-bipyridin-5yl)alanine is used to bind the catalytic Cu(ii) ion. Starting from a set of empirical pre-conditions, a combination of cluster model calculations (QM), protein-ligand docking and molecular dynamics simulations was used to propose metallohydratase variants, that were experimentally verified. The agreement observed between the computationally predicted and experimentally observed catalysis results demonstrates the power of the artificial metalloenzyme design approach presented here.
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Affiliation(s)
- Ivana Drienovská
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
| | - Lur Alonso-Cotchico
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Pietro Vidossich
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Agustí Lledós
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - 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 , Netherlands .
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44
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van der Velde JHM, Oelerich J, Huang J, Smit JH, Jazi AA, Galiani S, Kolmakov K, Gouridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T. Corrigendum: A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nat Commun 2017; 8:16144. [PMID: 28776565 PMCID: PMC5547757 DOI: 10.1038/ncomms16144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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45
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Abstract
Artificial metalloenzymes were created from multidrug resistance regulator proteins by in vivo incorporation of an unnatural metal binding amino acid.
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Affiliation(s)
- Manuela Bersellini
- 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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46
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Abstract
An artificial metalloenzyme containing both a regulatory and a catalytic domain is selectively activated in presence of Fe2+ ions.
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Affiliation(s)
- Manuela Bersellini
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
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47
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García-Fernández A, Megens RP, Villarino L, Roelfes G. DNA-Accelerated Copper Catalysis of Friedel–Crafts Conjugate Addition/Enantioselective Protonation Reactions in Water. J Am Chem Soc 2016; 138:16308-16314. [DOI: 10.1021/jacs.6b08295] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Almudena García-Fernández
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG, Groningen, The Netherlands
| | - Rik P. Megens
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG, Groningen, The Netherlands
| | - Lara Villarino
- 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
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48
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Rioz-Martínez A, Oelerich J, Ségaud N, Roelfes G. DNA-Accelerated Catalysis of Carbene-Transfer Reactions by a DNA/Cationic Iron Porphyrin Hybrid. Angew Chem Int Ed Engl 2016; 55:14136-14140. [PMID: 27730731 PMCID: PMC5113691 DOI: 10.1002/anie.201608121] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 11/16/2022]
Abstract
A novel DNA-based hybrid catalyst comprised of salmon testes DNA and an iron(III) complex of a cationic meso-tetrakis(N-alkylpyridyl)porphyrin was developed. When the N-methyl substituents were placed at the ortho position with respect to the porphyrin ring, high reactivity in catalytic carbene-transfer reactions was observed under mild conditions, as demonstrated in the catalytic enantioselective cyclopropanation of styrene derivatives with ethyl diazoacetate (EDA) as the carbene precursor. A remarkable feature of this catalytic system is the large DNA-induced rate acceleration observed in this reaction and the related dimerization of EDA. It is proposed that high effective molarity of all components of the reaction in or near the DNA is one of the key contributors to this unique reactivity. This study demonstrates that the concept of DNA-based asymmetric catalysis can be expanded into the realm of organometallic chemistry.
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Affiliation(s)
- Ana Rioz-Martínez
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jens Oelerich
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nathalie Ségaud
- 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.
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49
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Rioz-Martínez A, Oelerich J, Ségaud N, Roelfes G. DNA-Accelerated Catalysis of Carbene-Transfer Reactions by a DNA/Cationic Iron Porphyrin Hybrid. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ana Rioz-Martínez
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jens Oelerich
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Nathalie Ségaud
- 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
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50
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van der Velde JHM, Oelerich J, Huang J, Smit JH, Aminian Jazi A, Galiani S, Kolmakov K, Guoridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nat Commun 2016; 7:10144. [PMID: 26751640 PMCID: PMC4729898 DOI: 10.1038/ncomms10144] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/05/2015] [Indexed: 11/09/2022] Open
Abstract
Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.
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Affiliation(s)
- Jasper H M van der Velde
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jens Oelerich
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jingyi Huang
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Atieh Aminian Jazi
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Kirill Kolmakov
- Department NanoBiophotonics, Max-Planck-Institute of Molecular Medicine, Am Fassberg 1, 37077 Goettingen, Germany
| | - Giorgos Guoridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Andreas Herrmann
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, 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
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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