1
|
Gay R, Masson Y, Ghattas W, Udry GAO, Herrero C, Urvoas A, Mahy JP, Ricoux R. Binding and Stabilization of a Semiquinone Radical by an Artificial Metalloenzyme Containing a Binuclear Copper (II) Cofactor. Chembiochem 2024:e202400139. [PMID: 38682718 DOI: 10.1002/cbic.202400139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/01/2024]
Abstract
A binuclear Cu(II) cofactor was covalently bound to a lauric acid anchor. The resulting conjugate was characterized then combined with beta-lactoglobulin (βLG) to generate a new biohybrid following the so-called "Trojan horse" strategy. This biohybrid was examined for its effectiveness in the oxidation of a catechol derivative to the corresponding quinone. The resulting biohybrid did not exhibit the sought after catecholase activity, likely due to its ability to bind and stabilize the semiquinone radical intermediate DTB-SQ. This semi-quinone radical was stabilized only in the presence of the protein and was characterized using optical and magnetic spectroscopic techniques, demonstrating stability for over 16 hours. Molecular docking studies revealed that this stabilization could occur owing to interactions of the semi-quinone with hydrophobic amino acid residues of βLG.
Collapse
Affiliation(s)
- Rémy Gay
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Yannick Masson
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Wadih Ghattas
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Guillermo A Oliveira Udry
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Christian Herrero
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Bât. 21, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Jean-Pierre Mahy
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Rémy Ricoux
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| |
Collapse
|
2
|
Lee J, Kim M, Lee H, Lee SY. Rh-coordinated histidyl bolaamphiphile assembly: a catalyst for the isomerization of cis-stilbene and cis-alkene. Dalton Trans 2023; 52:13269-13277. [PMID: 37668062 DOI: 10.1039/d3dt01906c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
In this study, we present a colloidal assembly of histidyl bolaamphiphiles whose imidazoles coordinate with rhodium ions (HisC7[Rh]) to exhibit catalytic isomerization activity for cis-stilbene and cis-alkene molecules. The histidyl bolaamphiphiles self-assemble to form a soft scaffold that functions analogously to an apoenzyme. This scaffold exposes multiple histidyl imidazoles and carboxylates on its surface, to which rhodium ions bind, generating catalytically active sites. The Rh coordination with the biochemical functional groups was verified through comprehensive vibrational spectroscopy and calorimetry. The colloidal HisC7[Rh] demonstrated a significant catalytic effect on the isomerization of cis- to trans-stilbene under mild H2 conditions, resulting in 69% yield of trans-stilbene. In contrast, when Rh(cod)2BF4 was employed as a control catalyst, only the hydrogenated products of bibenzyl were obtained. These findings underscore the crucial role of histidyl motifs in exhibiting unique catalytic isomerization activity through the coordination with Rh. The catalytic activity of HisC7[Rh] is governed by several factors, such as rhodium content, solvent composition, temperature, and H2 pressure. Moreover, HisC7[Rh] displayed moderate isomerization activity towards not only stilbene but also unsaturated fatty acid isomers, highlighting its expansive potential as an isomerization catalyst.
Collapse
Affiliation(s)
- Junsang Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Minji Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Hyesung Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Sang-Yup Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Marsden SR, Wijma HJ, Mohr MKF, Justo I, Hagedoorn P, Laustsen J, Jeffries CM, Svergun D, Mestrom L, McMillan DGG, Bento I, Hanefeld U. Substrate Induced Movement of the Metal Cofactor between Active and Resting State. Angew Chem Int Ed Engl 2022; 61:e202213338. [PMID: 36214476 PMCID: PMC10099721 DOI: 10.1002/anie.202213338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 11/11/2022]
Abstract
Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. In its resting state configuration (M2+ R ), the metal constitutes an integral part of the dimer interface within the overall hexameric assembly, but sterical constraints do not allow for substrate binding. Conversely, a second coordination sphere constitutes the catalytically active state (M2+ A ) at 2.4 Å distance. Bidentate coordination of a ketoacid substrate to M2+ A affords the overall lowest energy complex, which drives the transition from M2+ R to M2+ A . While not described earlier, this type of regulation may be widespread and largely overlooked due to low occupancy of some of its states in protein crystal structures.
Collapse
Affiliation(s)
- Stefan R. Marsden
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Hein J. Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute Faculty of Science and Engineering University of Groningen Nijenborg 4 9747AG Groningen The Netherlands
| | - Michael K. F. Mohr
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Inês Justo
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Peter‐Leon Hagedoorn
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | | | | | | | - Luuk Mestrom
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Duncan G. G. McMillan
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| | - Isabel Bento
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Ulf Hanefeld
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft The Netherlands
| |
Collapse
|
5
|
An artificial metalloprotein with metal-adaptive coordination sites and Ni-dependent quercetinase activity. J Inorg Biochem 2022; 235:111914. [PMID: 35841720 DOI: 10.1016/j.jinorgbio.2022.111914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/20/2022] [Accepted: 07/03/2022] [Indexed: 11/23/2022]
Abstract
Engineering non-native metal active sites into proteins using canonical amino acids offers many advantages but is hampered by significant challenges. The TIM barrel protein, imidazole glycerol phosphate synthase from the hyperthermophilic organism Thermotoga maritima (tHisF), is well-suited for the construction of artificial metalloenzymes by this approach. To this end, we have generated a tHisF variant (tHisFEHH) with a Glu/His/His motif for metal ion coordination. Crystal structures of ZnII:tHisFEHH and NiII:tHisFEHH reveal that both metal ions bind to the engineered histidines. However, the two metals bind at distinct sites with different geometries, demonstrating the adaptability of tHisF. Only ZnII additionally ligates the Glu residue and adopts a tetrahedral geometry. The pseudo-octahedral NiII site comprises the two His and a native Ser residue. NiII:tHisFEHH catalyzes the oxidative cleavage of the flavanols quercetin and myricetin, providing an unprecedented example of an artificial metalloprotein with quercetinase activity.
Collapse
|
6
|
Zhao K, Wang X, He D, Wang H, Qian B, Shi F. Recent development towards alkene hydroformylation catalysts integrating traditional homo- and heterogeneous catalysis. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00845a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This mini-review provides the recent progress towards catalysts for the hydroformylation of catalysts that bridge traditional homo- and heterogeneous catalysis, highlighting the future development of heterogeneous catalysts in hydroformylation.
Collapse
Affiliation(s)
- Kang Zhao
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, No.18, Tianshui Middle Road, Lanzhou, 730000, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A, Yuquanlu, Beijing, 100049, People's Republic of China
| | - Xinzhi Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, No.18, Tianshui Middle Road, Lanzhou, 730000, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A, Yuquanlu, Beijing, 100049, People's Republic of China
| | - Dongcheng He
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, No.18, Tianshui Middle Road, Lanzhou, 730000, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A, Yuquanlu, Beijing, 100049, People's Republic of China
| | - Hongli Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, No.18, Tianshui Middle Road, Lanzhou, 730000, People's Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People's Republic of China
| | - Bo Qian
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, No.18, Tianshui Middle Road, Lanzhou, 730000, People's Republic of China
| | - Feng Shi
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, No.18, Tianshui Middle Road, Lanzhou, 730000, People's Republic of China
| |
Collapse
|
7
|
Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
Collapse
Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
8
|
Biggs GS, Klein OJ, Maslen SL, Skehel JM, Rutherford TJ, Freund SMV, Hollfelder F, Boss SR, Barker PD. Controlled Ligand Exchange Between Ruthenium Organometallic Cofactor Precursors and a Naïve Protein Scaffold Generates Artificial Metalloenzymes Catalysing Transfer Hydrogenation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015834] [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)
- George S. Biggs
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Oskar James Klein
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Sarah L. Maslen
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - J. Mark Skehel
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Trevor J. Rutherford
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Stefan M. V. Freund
- MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Florian Hollfelder
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Sally R. Boss
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Paul D. Barker
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
9
|
Biggs GS, Klein OJ, Maslen SL, Skehel JM, Rutherford TJ, Freund SMV, Hollfelder F, Boss SR, Barker PD. Controlled Ligand Exchange Between Ruthenium Organometallic Cofactor Precursors and a Naïve Protein Scaffold Generates Artificial Metalloenzymes Catalysing Transfer Hydrogenation. Angew Chem Int Ed Engl 2021; 60:10919-10927. [PMID: 33616271 PMCID: PMC8251807 DOI: 10.1002/anie.202015834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 11/05/2022]
Abstract
Many natural metalloenzymes assemble from proteins and biosynthesised complexes, generating potent catalysts by changing metal coordination. Here we adopt the same strategy to generate artificial metalloenzymes (ArMs) using ligand exchange to unmask catalytic activity. By systematically testing RuII (η6 -arene)(bipyridine) complexes designed to facilitate the displacement of functionalised bipyridines, we develop a fast and robust procedure for generating new enzymes via ligand exchange in a protein that has not evolved to bind such a complex. The resulting metal cofactors form peptidic coordination bonds but also retain a non-biological ligand. Tandem mass spectrometry and 19 F NMR spectroscopy were used to characterise the organometallic cofactors and identify the protein-derived ligands. By introduction of ruthenium cofactors into a 4-helical bundle, transfer hydrogenation catalysts were generated that displayed a 35-fold rate increase when compared to the respective small molecule reaction in solution.
Collapse
Affiliation(s)
- George S. Biggs
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Oskar James Klein
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1GAUK
| | - Sarah L. Maslen
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - J. Mark Skehel
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Trevor J. Rutherford
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Stefan M. V. Freund
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Florian Hollfelder
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1GAUK
| | - Sally R. Boss
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Paul D. Barker
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| |
Collapse
|
10
|
Basle M, Padley HAW, Martins FL, Winkler GS, Jäger CM, Pordea A. Design of artificial metalloenzymes for the reduction of nicotinamide cofactors. J Inorg Biochem 2021; 220:111446. [PMID: 33865209 DOI: 10.1016/j.jinorgbio.2021.111446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022]
Abstract
Artificial metalloenzymes result from the insertion of a catalytically active metal complex into a biological scaffold, generally a protein devoid of other catalytic functionalities. As such, their design requires efforts to engineer substrate binding, in addition to accommodating the artificial catalyst. Here we constructed and characterised artificial metalloenzymes using alcohol dehydrogenase as starting point, an enzyme which has both a cofactor and a substrate binding pocket. A docking approach was used to determine suitable positions for catalyst anchoring to single cysteine mutants, leading to an artificial metalloenzyme capable to reduce both natural cofactors and the hydrophobic 1-benzylnicotinamide mimic. Kinetic studies revealed that the new construct displayed a Michaelis-Menten behaviour with the native nicotinamide cofactors, which were suggested by docking to bind at a surface exposed site, different compared to their native binding position. On the other hand, the kinetic and docking data suggested that a typical enzyme behaviour was not observed with the hydrophobic 1-benzylnicotinamide mimic, with which binding events were plausible both inside and outside the protein. This work demonstrates an extended substrate scope of the artificial metalloenzymes and provides information about the binding sites of the nicotinamide substrates, which can be exploited to further engineer artificial metalloenzymes for cofactor regeneration. SYNOPSIS ABOUT GRAPHICAL ABSTRACT: The manuscript provides information on the design of artificial metalloenzymes based on the bioconjugation of rhodium complexes to alcohol dehydrogenase, to improve their ability to reduce hydrophobic substrates. The graphical abstract presents different binding modes and results observed with native cofactors as substrates, compared to the hydrophobic benzylnicotinamide.
Collapse
Affiliation(s)
- Mattias Basle
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Henry A W Padley
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Floriane L Martins
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | | | - Christof M Jäger
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Anca Pordea
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom.
| |
Collapse
|
11
|
Abiotic reduction of ketones with silanes catalysed by carbonic anhydrase through an enzymatic zinc hydride. Nat Chem 2021; 13:312-318. [PMID: 33603222 PMCID: PMC8675236 DOI: 10.1038/s41557-020-00633-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Enzymatic reactions through mononuclear metal hydrides are unknown in nature, despite the prevalence of such intermediates in the reactions of synthetic transition-metal catalysts. If metalloenzymes would react through abiotic intermediates like these, then the scope of enzyme-catalyzed reactions would expand. Here we show that zinc-containing carbonic anhydrase enzymes catalyze hydride transfers from silanes to ketones with high enantioselectivity and report mechanistic data providing strong evidence that the process involves a mononuclear zinc hydride. This work shows that abiotic silanes can act as reducing equivalents in an enzyme-catalyzed process and that monomeric hydrides of electropositive metals, which are typically unstable in protic environments, can be catalytic intermediates in enzymatic processes. Overall, this work bridges a gap between the types of transformations in molecular catalysis and biocatalysis.
Collapse
|
12
|
Ma D, Xie H, Cao Z. Catalytic Coupling of CH4 with CO2 and CO by a Modified Human Carbonic Anhydrase Combined with Oriented External Electric Fields: Mechanistic Insights from DFT Calculations. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Denghui Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
| | - Hujun Xie
- Department of Applied Chemistry, Zhejiang Gongshang University, Hangzhou 310018, People’s Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
| |
Collapse
|
13
|
Villarino L, Chordia S, Alonso-Cotchico L, Reddem E, Zhou Z, Thunnissen AMWH, Maréchal JD, Roelfes G. Cofactor Binding Dynamics Influence the Catalytic Activity and Selectivity of an Artificial Metalloenzyme. ACS Catal 2020; 10:11783-11790. [PMID: 33101759 PMCID: PMC7574625 DOI: 10.1021/acscatal.0c01619] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/11/2020] [Indexed: 12/20/2022]
Abstract
We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits dynamics involving the positioning of its abiological metal cofactor. The position of the cofactor, in turn, was found to be related to the preferred catalytic reactivity, which is either the enantioselective Friedel-Crafts alkylation of indoles with β-substituted enones or the tandem Friedel-Crafts alkylation/enantioselective protonation of indoles with α-substituted enones. The artificial metalloenzyme could be specialized for one of these catalytic reactions introducing a single mutation in the protein. The relation between cofactor dynamics and activity and selectivity in catalysis has not been described for natural enzymes and, to date, appears to be particular for artificial metalloenzymes.
Collapse
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
| |
Collapse
|
14
|
Biggs GS, Klein OJ, Boss SR, Barker PD. Unlocking the Full Evolutionary Potential of Artificial Metalloenzymes Through Direct Metal-Protein Coordination : A review of recent advances for catalyst development. JOHNSON MATTHEY TECHNOLOGY REVIEW 2020. [DOI: 10.1595/205651320x15928204097766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Generation of artificial metalloenzymes (ArMs) has gained much inspiration from the general understanding of natural metalloenzymes. Over the last decade, a multitude of methods generating transition metal-protein hybrids have been developed and many of these new-to-nature constructs
catalyse reactions previously reserved for the realm of synthetic chemistry. This perspective will focus on ArMs incorporating 4d and 5d transition metals. It aims to summarise the significant advances made to date and asks whether there are chemical strategies, used in nature to optimise
metal catalysts, that have yet to be fully recognised in the synthetic enzyme world, particularly whether artificial enzymes produced to date fully take advantage of the structural and energetic context provided by the protein. Further, the argument is put forward that, based on precedence,
in the majority of naturally evolved metalloenzymes the direct coordination bonding between the metal and the protein scaffold is integral to catalysis. Therefore, the protein can attenuate metal activity by positioning ligand atoms in the form of amino acids, as well as making non-covalent
contributions to catalysis, through intermolecular interactions that pre-organise substrates and stabilise transition states. This highlights the often neglected but crucial element of natural systems that is the energetic contribution towards activating metal centres through protein fold
energy. Finally, general principles needed for a different approach to the formation of ArMs are set out, utilising direct coordination inspired by the activation of an organometallic cofactor upon protein binding. This methodology, observed in nature, delivers true interdependence between
metal and protein. When combined with the ability to efficiently evolve enzymes, new problems in catalysis could be addressed in a faster and more specific manner than with simpler small molecule catalysts.
Collapse
Affiliation(s)
- George S. Biggs
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW UK
| | - Oskar James Klein
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW UK
| | - Sally R. Boss
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW UK
| | - Paul D. Barker
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW UK
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Abstract
Metalloenzymes such as the carbonic anhydrases (CAs, EC 4.2.1.1) possess highly specialized active sites that promote fast reaction rates and high substrate selectivity for the physiologic reaction that they catalyze, hydration of CO2 to bicarbonate and a proton. Among the eight genetic CA macrofamilies, α-CAs possess rather spacious active sites and show catalytic promiscuity, being esterases with many types of esters, but also acting on diverse small molecules such as cyanamide, carbonyl sulfide (COS), CS2, etc. Although artificial CAs have been developed with the intent to efficiently catalyse non-biologically related chemical transformations with high control of stereoselectivity, the activities of these enzymes were much lower when compared to natural CAs. Here, we report an overview on the catalytic activities of α-CAs as well as of enzymes which were mutated or artificially designed by incorporation of transition metal ions. In particular, the distinct catalytic mechanisms of the reductase, oxidase and metatheses-ase such as de novo designed CAs are discussed.
Collapse
|
17
|
Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
Collapse
Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| |
Collapse
|
18
|
|
19
|
Leveson-Gower RB, Mayer C, Roelfes G. The importance of catalytic promiscuity for enzyme design and evolution. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0143-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
20
|
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
| | | |
Collapse
|
21
|
Davis H, Ward TR. Artificial Metalloenzymes: Challenges and Opportunities. ACS CENTRAL SCIENCE 2019; 5:1120-1136. [PMID: 31404244 PMCID: PMC6661864 DOI: 10.1021/acscentsci.9b00397] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Indexed: 05/04/2023]
Abstract
Artificial metalloenzymes (ArMs) result from the incorporation of an abiotic metal cofactor within a protein scaffold. From the earliest techniques of transition metals adsorbed on silk fibers, the field of ArMs has expanded dramatically over the past 60 years to encompass a range of reaction classes and inspired approaches: Assembly of the ArMs has taken multiple forms with both covalent and supramolecular anchoring strategies, while the scaffolds have been intuitively selected and evolved, repurposed, or designed in silico. Herein, we discuss some of the most prominent recent examples of ArMs to highlight the challenges and opportunities presented by the field.
Collapse
|
22
|
Imam HT, Jarvis AG, Celorrio V, Baig I, Allen CCR, Marr AC, Kamer PCJ. Catalytic and biophysical investigation of rhodium hydroformylase. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01679a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rh-Containing artificial metalloenzymes based on two mutants of sterol carrier protein_2L (SCP_2L) have been shown to act as hydroformylases, exhibiting significant activity and unexpectedly high selectivity in the hydroformylation of alkenes.
Collapse
Affiliation(s)
- Hasan T. Imam
- School of Chemistry
- University of St Andrews
- St Andrews
- UK
- School of Chemistry and Chemical Engineering
| | | | | | - Irshad Baig
- School of Chemistry
- University of St Andrews
- St Andrews
- UK
| | | | - Andrew C. Marr
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
| | - Paul C. J. Kamer
- Bioinspired Homo- & Heterogeneous Catalysis
- Leibniz Institute for Catalysis
- Rostock
- Germany
| |
Collapse
|
23
|
Hayashi T, Hilvert D, Green AP. Engineered Metalloenzymes with Non-Canonical Coordination Environments. Chemistry 2018; 24:11821-11830. [PMID: 29786902 DOI: 10.1002/chem.201800975] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/09/2022]
Abstract
Nature employs a limited number of genetically encoded, metal-coordinating residues to create metalloenzymes with diverse structures and functions. Engineered components of the cellular translation machinery can now be exploited to encode non-canonical ligands with user-defined electronic and structural properties. This ability to install "chemically programmed" ligands into proteins can provide powerful chemical probes of metalloenzyme mechanism and presents excellent opportunities to create metalloprotein catalysts with augmented properties and novel activities. In this Concept article, we provide an overview of several recent studies describing the creation of engineered metalloenzymes with interesting catalytic properties, and reveal how characterization of these systems has advanced our understanding of nature's bioinorganic mechanisms. We also highlight how powerful laboratory evolution protocols can be readily adapted to allow optimization of metalloenzymes with non-canonical ligands. This approach combines beneficial features of small molecule and protein catalysis by allowing the installation of a greater variety of local metal coordination environments into evolvable protein scaffolds, and holds great promise for the future creation of powerful metalloprotein catalysts for a host of synthetically valuable transformations.
Collapse
Affiliation(s)
- Takahiro Hayashi
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anthony P Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| |
Collapse
|
24
|
de Jesús Cázares-Marinero J, Przybylski C, Salmain M. Proteins as Macromolecular Ligands for Metal-Catalysed Asymmetric Transfer Hydrogenation of Ketones in Aqueous Medium. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201701359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | - Cédric Przybylski
- Institut Parisien de Chimie Moléculaire, IPCM; Sorbonne Université, CNRS; 75005 Paris France
| | - Michèle Salmain
- Institut Parisien de Chimie Moléculaire, IPCM; Sorbonne Université, CNRS; 75005 Paris France
| |
Collapse
|
25
|
Pandey S, Raj KV, Shinde DR, Vanka K, Kashyap V, Kurungot S, Vinod CP, Chikkali SH. Iron Catalyzed Hydroformylation of Alkenes under Mild Conditions: Evidence of an Fe(II) Catalyzed Process. J Am Chem Soc 2018. [DOI: 10.1021/jacs.8b01286] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Swechchha Pandey
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - K. Vipin Raj
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Dinesh R. Shinde
- Central NMR Facility, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Kumar Vanka
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Varchaswal Kashyap
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Sreekumar Kurungot
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - C. P. Vinod
- Catalysis Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Samir H. Chikkali
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110001, India
| |
Collapse
|
26
|
Reynolds EW, Schwochert TD, McHenry MW, Watters JW, Brustad EM. Orthogonal Expression of an Artificial Metalloenzyme for Abiotic Catalysis. Chembiochem 2017; 18:2380-2384. [PMID: 29024391 PMCID: PMC5875912 DOI: 10.1002/cbic.201700397] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Indexed: 11/08/2022]
Abstract
A cytochrome P450 was engineered to selectively incorporate Ir(Me)-deuteroporphyrin IX (Ir(Me)-DPIX), in lieu of heme, in bacterial cells. Cofactor selectivity was altered by introducing mutations within the heme-binding pocket to discriminate the deuteroporphyrin macrocycle, in combination with mutations to the P450 axial cysteine to accommodate a pendant methyl group on the Ir(Me) center. This artificial metalloenzyme was investigated for activity in non-native metallocarbenoid-mediated olefin cyclopropanation reactions and showed enhanced activity for aliphatic and electron-deficient olefins when compared to the native heme enzyme. This work provides a general strategy to augment the chemical functionality of heme enzymes in cells with application towards abiotic catalysis.
Collapse
Affiliation(s)
- Evan W Reynolds
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road CB 3290, Chapel Hill, North Carolina, 27599, USA
| | - Timothy D Schwochert
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road CB 3290, Chapel Hill, North Carolina, 27599, USA
| | - Matthew W McHenry
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road CB 3290, Chapel Hill, North Carolina, 27599, USA
| | - John W Watters
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road CB 3290, Chapel Hill, North Carolina, 27599, USA
| | - Eric M Brustad
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road CB 3290, Chapel Hill, North Carolina, 27599, USA
| |
Collapse
|
27
|
Bozkurt E, Soares TA, Rothlisberger U. Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective. J Chem Theory Comput 2017; 13:6382-6390. [DOI: 10.1021/acs.jctc.7b00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esra Bozkurt
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Thereza A. Soares
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Fundamental Chemistry, Federal University of Pernambuco, Recife 50740-560, Brazil
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
28
|
|
29
|
Jarvis AG, Obrecht L, Deuss PJ, Laan W, Gibson EK, Wells PP, Kamer PCJ. Enzyme Activity by Design: An Artificial Rhodium Hydroformylase for Linear Aldehydes. Angew Chem Int Ed Engl 2017; 56:13596-13600. [PMID: 28841767 PMCID: PMC5659135 DOI: 10.1002/anie.201705753] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 01/14/2023]
Abstract
Artificial metalloenzymes (ArMs) are hybrid catalysts that offer a unique opportunity to combine the superior performance of natural protein structures with the unnatural reactivity of transition‐metal catalytic centers. Therefore, they provide the prospect of highly selective and active catalytic chemical conversions for which natural enzymes are unavailable. Herein, we show how by rationally combining robust site‐specific phosphine bioconjugation methods and a lipid‐binding protein (SCP‐2L), an artificial rhodium hydroformylase was developed that displays remarkable activities and selectivities for the biphasic production of long‐chain linear aldehydes under benign aqueous conditions. Overall, this study demonstrates that judiciously chosen protein‐binding scaffolds can be adapted to obtain metalloenzymes that provide the reactivity of the introduced metal center combined with specifically intended product selectivity.
Collapse
Affiliation(s)
- Amanda G Jarvis
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Lorenz Obrecht
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Peter J Deuss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.,Department of Chemical Engineering (ENTEG), University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Wouter Laan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.,Current address: Phoreon, Bioincubator I, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Emma K Gibson
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.,UK Catalysis Hub, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Peter P Wells
- UK Catalysis Hub, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0FA, UK.,School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.,Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Paul C J Kamer
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.,Bioinspired Homo- & Heterogeneous Catalysis, Leibniz Institute for Catalysis, Albert-Einstein-Strasse 29a, 18059, Rostock, Germany
| |
Collapse
|
30
|
Jarvis AG, Obrecht L, Deuss PJ, Laan W, Gibson EK, Wells PP, Kamer PCJ. Enzyme Activity by Design: An Artificial Rhodium Hydroformylase for Linear Aldehydes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Amanda G. Jarvis
- School of Chemistry; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
| | - Lorenz Obrecht
- School of Chemistry; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
| | - Peter J. Deuss
- School of Chemistry; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
- Department of Chemical Engineering (ENTEG); University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wouter Laan
- School of Chemistry; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
- Current address: Phoreon; Bioincubator I; Gaston Geenslaan 1 3001 Leuven Belgium
| | - Emma K. Gibson
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
- UK Catalysis Hub; Research Complex at Harwell; Rutherford Appleton Laboratory; Harwell Science & Innovation Campus; Didcot Oxfordshire OX11 0FA UK
| | - Peter P. Wells
- UK Catalysis Hub; Research Complex at Harwell; Rutherford Appleton Laboratory; Harwell Science & Innovation Campus; Didcot Oxfordshire OX11 0FA UK
- School of Chemistry; University of Southampton; Southampton SO17 1BJ UK
- Diamond Light Source; Harwell Science & Innovation Campus; Didcot Oxfordshire OX11 0DE UK
| | - Paul C. J. Kamer
- School of Chemistry; University of St Andrews; North Haugh St Andrews Fife KY16 9ST UK
- Bioinspired Homo- & Heterogeneous Catalysis; Leibniz Institute for Catalysis; Albert-Einstein-Strasse 29a 18059 Rostock Germany
| |
Collapse
|
31
|
Piazzetta P, Marino T, Russo N, Salahub DR. The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
32
|
Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 475] [Impact Index Per Article: 67.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
Collapse
Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| |
Collapse
|
33
|
Fujieda N, Nakano T, Taniguchi Y, Ichihashi H, Sugimoto H, Morimoto Y, Nishikawa Y, Kurisu G, Itoh S. A Well-Defined Osmium–Cupin Complex: Hyperstable Artificial Osmium Peroxygenase. J Am Chem Soc 2017; 139:5149-5155. [DOI: 10.1021/jacs.7b00675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nobutaka Fujieda
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Takumi Nakano
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuki Taniguchi
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Haruna Ichihashi
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hideki Sugimoto
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuma Morimoto
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yosuke Nishikawa
- Institute
for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Institute
for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shinobu Itoh
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
34
|
Piazzetta P, Marino T, Russo N, Salahub DR. Explicit Water Molecules Play a Key Role in the Mechanism of Rhodium-Substituted Human Carbonic Anhydrase. ChemCatChem 2017. [DOI: 10.1002/cctc.201601433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Paolo Piazzetta
- Dipartimento di Chimica e Tecnologie Chimiche (CTC); Universitá della Calabria; 87036 Arcavacata di Rende CS Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche (CTC); Universitá della Calabria; 87036 Arcavacata di Rende CS Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche (CTC); Universitá della Calabria; 87036 Arcavacata di Rende CS Italy
| | - Dennis R. Salahub
- Department of Chemistry; Institute for Quantum Science and Technology; Centre for Molecular Simulation, BI 556; University of Calgary; 2500 University Drive NW Calgary Alberta T2N 1N4 Canada
| |
Collapse
|
35
|
|
36
|
Key HM, Dydio P, Clark DS, Hartwig JF. Abiological catalysis by artificial haem proteins containing noble metals in place of iron. Nature 2016; 534:534-7. [PMID: 27296224 DOI: 10.1038/nature17968] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022]
Abstract
Enzymes that contain metal ions--that is, metalloenzymes--possess the reactivity of a transition metal centre and the potential of molecular evolution to modulate the reactivity and substrate-selectivity of the system. By exploiting substrate promiscuity and protein engineering, the scope of reactions catalysed by native metalloenzymes has been expanded recently to include abiological transformations. However, this strategy is limited by the inherent reactivity of metal centres in native metalloenzymes. To overcome this limitation, artificial metalloproteins have been created by incorporating complete, noble-metal complexes within proteins lacking native metal sites. The interactions of the substrate with the protein in these systems are, however, distinct from those with the native protein because the metal complex occupies the substrate binding site. At the intersection of these approaches lies a third strategy, in which the native metal of a metalloenzyme is replaced with an abiological metal with reactivity different from that of the metal in a native protein. This strategy could create artificial enzymes for abiological catalysis within the natural substrate binding site of an enzyme that can be subjected to directed evolution. Here we report the formal replacement of iron in Fe-porphyrin IX (Fe-PIX) proteins with abiological, noble metals to create enzymes that catalyse reactions not catalysed by native Fe-enzymes or other metalloenzymes. In particular, we prepared modified myoglobins containing an Ir(Me) site that catalyse the functionalization of C-H bonds to form C-C bonds by carbene insertion and add carbenes to both β-substituted vinylarenes and unactivated aliphatic α-olefins. We conducted directed evolution of the Ir(Me)-myoglobin and generated mutants that form either enantiomer of the products of C-H insertion and catalyse the enantio- and diastereoselective cyclopropanation of unactivated olefins. The presented method of preparing artificial haem proteins containing abiological metal porphyrins sets the stage for the generation of artificial enzymes from innumerable combinations of PIX-protein scaffolds and unnatural metal cofactors to catalyse a wide range of abiological transformations.
Collapse
Affiliation(s)
- Hanna M Key
- Department of Chemistry, University of California, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Paweł Dydio
- Department of Chemistry, University of California, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| |
Collapse
|
37
|
|
38
|
Keum C, Kim MC, Lee SY. Effects of transition metal ions on the catalytic activity of carbonic anhydrase mimics. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcata.2015.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
39
|
Piazzetta P, Marino T, Russo N, Salahub DR. Direct Hydrogenation of Carbon Dioxide by an Artificial Reductase Obtained by Substituting Rhodium for Zinc in the Carbonic Anhydrase Catalytic Center. A Mechanistic Study. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00185] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- P. Piazzetta
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, 87036Rende, Italy
| | - T. Marino
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, 87036Rende, Italy
| | - N. Russo
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, 87036Rende, Italy
| | - D. R. Salahub
- Department
of Chemistry, IQST − Institute for Quantum Science and Technology,
CMS − Centre for Molecular Simulation, BI 556, University of Calgary, 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| |
Collapse
|
40
|
Key HM, Clark DS, Hartwig JF. Generation, Characterization, and Tunable Reactivity of Organometallic Fragments Bound to a Protein Ligand. J Am Chem Soc 2015; 137:8261-8. [DOI: 10.1021/jacs.5b04431] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hanna M. Key
- Department
of Chemistry, University of California, Berkeley, California 94720, United States,
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States,
| | - Douglas S. Clark
- Department
of Chemistry, University of California, Berkeley, California 94720, United States,
- Department
of Chemical and Biomolecular Engineering, Physical and Biological
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - John F. Hartwig
- Department
of Chemistry, University of California, Berkeley, California 94720, United States,
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States,
| |
Collapse
|
41
|
Pàmies O, Diéguez M, Bäckvall JE. Artificial Metalloenzymes in Asymmetric Catalysis: Key Developments and Future Directions. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500290] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
42
|
Pordea A. Metal-binding promiscuity in artificial metalloenzyme design. Curr Opin Chem Biol 2015; 25:124-32. [PMID: 25603469 DOI: 10.1016/j.cbpa.2014.12.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 01/16/2023]
Abstract
This review presents recent examples of metal-binding promiscuity in protein scaffolds and highlights the effect of metal variation on catalytic functionality. Naturally evolved binding sites, as well as unnatural amino acids and cofactors can bind a diverse range of metals, including non-biological transition elements. Computational screening and rational design have been successfully used to create promiscuous binding-sites. Incorporation of non-native metals into proteins expands the catalytic range of transformations catalysed by enzymes and enhances their potential for application in chemicals synthesis.
Collapse
Affiliation(s)
- Anca Pordea
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
| |
Collapse
|
43
|
Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | |
Collapse
|
44
|
Raynal M, Ballester P, Vidal-Ferran A, van Leeuwen PWNM. Supramolecular catalysis. Part 2: artificial enzyme mimics. Chem Soc Rev 2013; 43:1734-87. [PMID: 24365792 DOI: 10.1039/c3cs60037h] [Citation(s) in RCA: 663] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.
Collapse
Affiliation(s)
- Matthieu Raynal
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.
| | | | | | | |
Collapse
|
45
|
Yang H, Srivastava P, Zhang C, Lewis JC. A general method for artificial metalloenzyme formation through strain-promoted azide-alkyne cycloaddition. Chembiochem 2013; 15:223-7. [PMID: 24376040 DOI: 10.1002/cbic.201300661] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Indexed: 12/29/2022]
Abstract
Strain-promoted azide-alkyne cycloaddition (SPAAC) can be used to generate artificial metalloenzymes (ArMs) from scaffold proteins containing a p-azido-L-phenylalanine (Az) residue and catalytically active bicyclononyne-substituted metal complexes. The high efficiency of this reaction allows rapid ArM formation when using Az residues within the scaffold protein in the presence of cysteine residues or various reactive components of cellular lysate. In general, cofactor-based ArM formation allows the use of any desired metal complex to build unique inorganic protein materials. SPAAC covalent linkage further decouples the native function of the scaffold from the installation process because it is not affected by native amino acid residues; as long as an Az residue can be incorporated, an ArM can be generated. We have demonstrated the scope of this method with respect to both the scaffold and cofactor components and established that the dirhodium ArMs generated can catalyze the decomposition of diazo compounds and both Si-H and olefin insertion reactions involving these carbene precursors.
Collapse
Affiliation(s)
- Hao Yang
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
| | | | | | | |
Collapse
|
46
|
Duarte F, Amrein BA, Kamerlin SCL. Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys 2013; 15:11160-77. [PMID: 23728154 PMCID: PMC3693508 DOI: 10.1039/c3cp51179k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022]
Abstract
In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.
Collapse
Affiliation(s)
- Fernanda Duarte
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | - Beat Anton Amrein
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | | |
Collapse
|
47
|
Huisman GW, Collier SJ. On the development of new biocatalytic processes for practical pharmaceutical synthesis. Curr Opin Chem Biol 2013; 17:284-92. [DOI: 10.1016/j.cbpa.2013.01.017] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/18/2013] [Accepted: 01/23/2013] [Indexed: 12/01/2022]
|
48
|
Heinisch T, Langowska K, Tanner P, Reymond JL, Meier W, Palivan C, Ward TR. Fluorescence-Based Assay for the Optimization of the Activity of Artificial Transfer Hydrogenase within a Biocompatible Compartment. ChemCatChem 2013. [DOI: 10.1002/cctc.201200834] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
49
|
Monnard FW, Nogueira ES, Heinisch T, Schirmer T, Ward TR. Human carbonic anhydrase II as host protein for the creation of artificial metalloenzymes: the asymmetric transfer hydrogenation of imines. Chem Sci 2013. [DOI: 10.1039/c3sc51065d] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
50
|
Köhler V, Wilson YM, Dürrenberger M, Ghislieri D, Churakova E, Quinto T, Knörr L, Häussinger D, Hollmann F, Turner NJ, Ward TR. Synthetic cascades are enabled by combining biocatalysts with artificial metalloenzymes. Nat Chem 2012; 5:93-9. [DOI: 10.1038/nchem.1498] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/10/2012] [Indexed: 12/22/2022]
|