51
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Stucki A, Vallapurackal J, Ward TR, Dittrich PS. Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Jaicy Vallapurackal
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Thomas R. Ward
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
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52
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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
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53
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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.
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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
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54
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Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. J Am Chem Soc 2021; 143:3330-3339. [PMID: 33635059 PMCID: PMC8012002 DOI: 10.1021/jacs.0c10053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-αthioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
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Affiliation(s)
- Elise A Naudin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Alastair G McEwen
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Pierre Poussin-Courmontagne
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Jean-Louis Schmitt
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Catherine Birck
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
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55
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Structural resolution of switchable states of a de novo peptide assembly. Nat Commun 2021; 12:1530. [PMID: 33750792 PMCID: PMC7943578 DOI: 10.1038/s41467-021-21851-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally. So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.
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56
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Yu J, Yang J, Seok C, Song WJ. Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes. Chem Sci 2021; 12:5091-5101. [PMID: 34168770 PMCID: PMC8179601 DOI: 10.1039/d0sc06823c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Directed evolution has provided us with great opportunities and prospects in the synthesis of tailor-made proteins. It, however, often requires at least mid to high throughput screening, necessitating more effective strategies for laboratory evolution. We herein demonstrate that protein symmetry can be a versatile criterion for searching for promising hotspots for the directed evolution of de novo oligomeric enzymes. The randomization of symmetry-related residues located at the rotational axes of artificial metallo-β-lactamase yields drastic effects on catalytic activities, whereas that of non-symmetry-related, yet, proximal residues to the active site results in negligible perturbations. Structural and biochemical analysis of the positive hits indicates that seemingly trivial mutations at symmetry-related spots yield significant alterations in overall structures, metal-coordination geometry, and chemical environments of active sites. Our work implicates that numerous artificially designed and natural oligomeric proteins might have evolutionary advantages of propagating beneficial mutations using their global symmetry. Symmetry-related residues located at the rotational axes can be promising hotspots for the evolution of de novo oligomeric enzymes even though they are distantly located from the active site pocket.![]()
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Affiliation(s)
- Jaeseung Yu
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Jinsol Yang
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Chaok Seok
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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57
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Klein AS, Zeymer C. Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis. Protein Eng Des Sel 2021; 34:6150309. [PMID: 33635315 DOI: 10.1093/protein/gzab003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.
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Affiliation(s)
- Andreas S Klein
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
| | - Cathleen Zeymer
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
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58
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Substrate promiscuity of a de novo designed peroxidase. J Inorg Biochem 2021; 217:111370. [PMID: 33621939 DOI: 10.1016/j.jinorgbio.2021.111370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 11/20/2022]
Abstract
The design and construction of de novo enzymes offer potentially facile routes to exploiting powerful chemistries in robust, expressible and customisable protein frameworks, while providing insight into natural enzyme function. To this end, we have recently demonstrated extensive catalytic promiscuity in a heme-containing de novo protein, C45. The diverse transformations that C45 catalyses include substrate oxidation, dehalogenation and carbon‑carbon bond formation. Here we explore the substrate promiscuity of C45's peroxidase activity, screening the de novo enzyme against a panel of peroxidase and dehaloperoxidase substrates. Consistent with the function of natural peroxidases, C45 exhibits a broad spectrum of substrate activities with selectivity dictated primarily by the redox potential of the substrate, and by extension, the active oxidising species in peroxidase chemistry, compounds I and II. Though the comparison of these redox potentials provides a threshold for determining activity for a given substrate, substrate:protein interactions are also likely to play a significant role in determining electron transfer rates from substrate to heme, affecting the kinetic parameters of the enzyme. We also used biomolecular simulation to screen substrates against a computational model of C45 to identify potential interactions and binding sites. Several sites of interest in close proximity to the heme cofactor were discovered, providing insight into the catalytic workings of C45.
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59
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Abstract
What were the physico-chemical forces that drove the origins of life? We discuss four major prebiotic ‘discoveries’: persistent sampling of chemical reaction space; sequence-encodable foldable catalysts; assembly of functional pathways; and encapsulation and heritability. We describe how a ‘proteins-first’ world gives plausible mechanisms. We note the importance of hydrophobic and polar compositions of matter in these advances.
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Affiliation(s)
- K A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Chemistry, Stony Brook University, Stony Brook, NY, USA.,Department Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA
| | - L Agozzino
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
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60
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Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold. Nat Chem 2021; 13:231-235. [DOI: 10.1038/s41557-020-00628-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
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61
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Tong CL, Lee KH, Seelig B. De novo proteins from random sequences through in vitro evolution. Curr Opin Struct Biol 2021; 68:129-134. [PMID: 33517151 DOI: 10.1016/j.sbi.2020.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022]
Abstract
Natural proteins are the result of billions of years of evolution. The earliest predecessors of today's proteins are believed to have emerged from random polypeptides. While we have no means to determine how this process exactly happened, there is great interest in understanding how it reasonably could have happened. We are reviewing how researchers have utilized in vitro selection and molecular evolution methods to investigate plausible scenarios for the emergence of early functional proteins. The studies range from analyzing general properties and structural features of unevolved random polypeptides to isolating de novo proteins with specific functions from synthetic randomized sequence libraries or generating novel proteins by combining evolution with rational design. While the results are exciting, more work is needed to fully unravel the mechanisms that seeded protein-dominated biology.
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Affiliation(s)
- Cher Ling Tong
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Kun-Hwa Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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62
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Searching protein space for ancient sub-domain segments. Curr Opin Struct Biol 2021; 68:105-112. [PMID: 33476896 DOI: 10.1016/j.sbi.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/29/2020] [Indexed: 01/08/2023]
Abstract
Evolutionary processes that formed the current protein universe left their traces, among them homologous segments that recur, or are 'reused,' in multiple proteins. These reused segments, called 'themes,' can be found at various scales, the best known of which is the domain. Yet, recent studies have begun to focus on the evolutionary insights that can be derived from sub-domain-scale themes, which are candidates for traces of more ancient events. Characterizing these may provide clues to the emergence of domains. Particularly interesting are themes that are reused across dissimilar contexts, that is, where the rest of the protein domain differs. We survey computational studies identifying reused themes within different contexts at the sub-domain level.
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63
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Vornholt T, Christoffel F, Pellizzoni MM, Panke S, Ward TR, Jeschek M. Systematic engineering of artificial metalloenzymes for new-to-nature reactions. SCIENCE ADVANCES 2021; 7:eabe4208. [PMID: 33523952 DOI: 10.1126/sciadv.abe4208] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Artificial metalloenzymes (ArMs) catalyzing new-to-nature reactions could play an important role in transitioning toward a sustainable economy. While ArMs have been created for various transformations, attempts at their genetic optimization have been case specific and resulted mostly in modest improvements. To realize their full potential, methods to rapidly discover active ArM variants for ideally any reaction of interest are required. Here, we introduce a reaction-independent, automation-compatible platform, which relies on periplasmic compartmentalization in Escherichia coli to rapidly and reliably engineer ArMs based on the biotin-streptavidin technology. We systematically assess 400 ArM mutants for five bioorthogonal transformations involving different metals, reaction mechanisms, and reactants, which include novel ArMs for gold-catalyzed hydroamination and hydroarylation. Activity enhancements up to 15-fold highlight the potential of the systematic approach. Furthermore, we suggest smart screening strategies and build machine learning models that accurately predict ArM activity from sequence, which has crucial implications for future ArM development.
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Affiliation(s)
- Tobias Vornholt
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Fadri Christoffel
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Michela M Pellizzoni
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Thomas R Ward
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Markus Jeschek
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland.
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
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64
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Fahrig-Kamarauskait J, Würth-Roderer K, Thorbjørnsrud HV, Mailand S, Krengel U, Kast P. Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance. J Biol Chem 2020; 295:17514-17534. [PMID: 33453995 PMCID: PMC7762937 DOI: 10.1074/jbc.ra120.014924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Indexed: 11/06/2022] Open
Abstract
Chorismate mutase (CM), an essential enzyme at the branch-point of the shikimate pathway, is required for the biosynthesis of phenylalanine and tyrosine in bacteria, archaea, plants, and fungi. MtCM, the CM from Mycobacterium tuberculosis, has less than 1% of the catalytic efficiency of a typical natural CM and requires complex formation with 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase for high activity. To explore the full potential of MtCM for catalyzing its native reaction, we applied diverse iterative cycles of mutagenesis and selection, thereby raising kcat/Km 270-fold to 5 × 105m−1s−1, which is even higher than for the complex. Moreover, the evolutionarily optimized autonomous MtCM, which had 11 of its 90 amino acids exchanged, was stabilized compared with its progenitor, as indicated by a 9 °C increase in melting temperature. The 1.5 Å crystal structure of the top-evolved MtCM variant reveals the molecular underpinnings of this activity boost. Some acquired residues (e.g. Pro52 and Asp55) are conserved in naturally efficient CMs, but most of them lie beyond the active site. Our evolutionary trajectories reached a plateau at the level of the best natural enzymes, suggesting that we have exhausted the potential of MtCM. Taken together, these findings show that the scaffold of MtCM, which naturally evolved for mediocrity to enable inter-enzyme allosteric regulation of the shikimate pathway, is inherently capable of high activity.
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Affiliation(s)
| | | | | | - Susanne Mailand
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Oslo, Norway.
| | - Peter Kast
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland.
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65
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Jafarpour A, Gregersen S, Marciel Gomes R, Marcatili P, Hegelund Olsen T, Jacobsen C, Overgaard MT, Sørensen ADM. Biofunctionality of Enzymatically Derived Peptides from Codfish ( Gadus morhua) Frame: Bulk In Vitro Properties, Quantitative Proteomics, and Bioinformatic Prediction. Mar Drugs 2020; 18:E599. [PMID: 33260992 PMCID: PMC7759894 DOI: 10.3390/md18120599] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
Protein hydrolysates show great promise as bioactive food and feed ingredients and for valorization of side-streams from e.g., the fish processing industry. We present a novel approach for hydrolysate characterization that utilizes proteomics data for calculation of weighted mean peptide properties (length, molecular weight, and charge) and peptide-level abundance estimation. Using a novel bioinformatic approach for subsequent prediction of biofunctional properties of identified peptides, we are able to provide an unprecedented, in-depth characterization. The study further characterizes bulk emulsifying, foaming, and in vitro antioxidative properties of enzymatic hydrolysates derived from cod frame by application of Alcalase and Neutrase, individually and sequentially, as well as the influence of heat pre-treatment. All hydrolysates displayed comparable or higher emulsifying activity and stability than sodium caseinate. Heat-treatment significantly increased stability but showed a negative effect on the activity and degree of hydrolysis. Lower degrees of hydrolysis resulted in significantly higher chelating activity, while the opposite was observed for radical scavenging activity. Combining peptide abundance with bioinformatic prediction, we identified several peptides that are likely linked to the observed differences in bulk emulsifying properties. The study highlights the prospects of applying proteomics and bioinformatics for hydrolysate characterization and in food protein science.
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Affiliation(s)
- Ali Jafarpour
- Research Group for Bioactives-Analysis and Application, Division of Food Technology, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (R.M.G.); (C.J.); (A.-D.M.S.)
| | - Simon Gregersen
- Section for Biotechnology, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark;
| | - Rocio Marciel Gomes
- Research Group for Bioactives-Analysis and Application, Division of Food Technology, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (R.M.G.); (C.J.); (A.-D.M.S.)
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (P.M.); (T.H.O.)
| | - Tobias Hegelund Olsen
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (P.M.); (T.H.O.)
| | - Charlotte Jacobsen
- Research Group for Bioactives-Analysis and Application, Division of Food Technology, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (R.M.G.); (C.J.); (A.-D.M.S.)
| | - Michael Toft Overgaard
- Section for Biotechnology, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark;
| | - Ann-Dorit Moltke Sørensen
- Research Group for Bioactives-Analysis and Application, Division of Food Technology, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (R.M.G.); (C.J.); (A.-D.M.S.)
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66
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Shroff R, Cole AW, Diaz DJ, Morrow BR, Donnell I, Annapareddy A, Gollihar J, Ellington AD, Thyer R. Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning. ACS Synth Biol 2020; 9:2927-2935. [PMID: 33064458 DOI: 10.1021/acssynbio.0c00345] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the promise of deep learning accelerated protein engineering, examples of such improved proteins are scarce. Here we report that a 3D convolutional neural network trained to associate amino acids with neighboring chemical microenvironments can guide identification of novel gain-of-function mutations that are not predicted by energetics-based approaches. Amalgamation of these mutations improved protein function in vivo across three diverse proteins by at least 5-fold. Furthermore, this model provides a means to interrogate the chemical space within protein microenvironments and identify specific chemical interactions that contribute to the gain-of-function phenotypes resulting from individual mutations.
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Affiliation(s)
- Raghav Shroff
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Austin W. Cole
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Daniel J. Diaz
- The Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Barrett R. Morrow
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Isaac Donnell
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ankur Annapareddy
- US Army Research Laboratories − South, 2506 Speedway, Austin, Texas 78712, United States
| | - Jimmy Gollihar
- US Army Research Laboratories − South, 2506 Speedway, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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67
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Huang Y, Chen J, Zhu L, Ma K, Kang K, Yang M, Lu S, Yan M, Wan Y, Deng S. Electrochemiluminescence-Repurposed Abiological Catalysts in Full Protein Tag for Ultrasensitive Immunoassay. Anal Chem 2020; 92:14076-14084. [PMID: 32938180 DOI: 10.1021/acs.analchem.0c03114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Being announced as one of the "2019 Top Ten Emerging Technologies in Chemistry" by IUPAC, the directed evolution of artificial metalloenzymes has led to a broad scope of abiotic processes. Here, inspired by those key proteins in bioluminescence, a rudimentary expression of bio-electrochemiluminescent (ECL) macromolecules was achieved via the complexation of zinc proto-porphyrin IX (ZnPPIX) within apo-hemoglobin (apo-Hb). A high-yield monochromic irradiation at 644 nm could be provoked potentiostatically from the reconstituted holo-HbZnPPIX in solutions. Its secondary structure integrity was elucidated by UV and circular dichroism spectrometry, while voltammetry-hyphenated surface plasmon resonance authenticated its ligation conservativeness in electrical fields. Further conjugation with streptavidin rendered a homogeneous Janus fusion of both receptor and reporter domains, enabling a new abiological catalyst-linked ECL bioassay. On the other hand, singular ZnPPIX inside each tetrameric subunit of Hb accomplished an overall signal amplification without the bother of luminogenic heterojunctions. This pH-tolerant and non-photobleaching optics was essentialized to be the unique configuration interaction between Zn and O2, by which the direct electrochemistry of proteins catalyzed the transient progression of O2 → O2·- → O2* + hυ selectively. Such principle was implemented as a signal-on strategy for the determination of a characteristic cancer biomarker, the vascular endothelial growth factor, resulting in competent performance at a low detection limit of 0.6 pg·mL-1 and a wide calibration range along with good stability and reliability in real practices. This simple mutation repurposed the O2-transport Hb in the erythrocytes of almost all vertebrates into a cluster of oxidoreductases with intrinsic ECL activity, which would enrich the chromophore library. More importantly, its genetically engineered variants may come in handy in biomedical diagnosis and visual electrophysiology.
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Affiliation(s)
- Yaqi Huang
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.,School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jialiang Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Longyi Zhu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kefeng Ma
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kai Kang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Meng Yang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shaohui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Minchuan Yan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Ying Wan
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shengyuan Deng
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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68
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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.
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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
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69
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Affiliation(s)
- Zebediah C. Girvin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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70
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Jarvis AG. Designer metalloenzymes for synthetic biology: Enzyme hybrids for catalysis. Curr Opin Chem Biol 2020; 58:63-71. [PMID: 32768658 DOI: 10.1016/j.cbpa.2020.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/14/2020] [Accepted: 06/11/2020] [Indexed: 02/09/2023]
Abstract
Combining organometallics and biology has generated broad interest from scientists working on applications from in situ drug release to biocatalysis. Engineered enzymes and biohybrid catalysts (also referred to as artificial enzymes) have introduced a wide range of abiotic chemistry into biocatalysis. Predominantly, this work has concentrated on using these catalysts for single step in vitro reactions. However, the promise of using these hybrid catalysts in vivo and combining them with synthetic biology and metabolic engineering is vast. This report will briefly review recent advances in artificial metalloenzyme design, followed by summarising recent studies that have looked at the use of these hybrid catalysts in vivo and in enzymatic cascades, therefore exploring their potential for synthetic biology.
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Affiliation(s)
- Amanda G Jarvis
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK.
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71
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Longo LM, Despotović D, Weil-Ktorza O, Walker MJ, Jabłońska J, Fridmann-Sirkis Y, Varani G, Metanis N, Tawfik DS. Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. Proc Natl Acad Sci U S A 2020; 117:15731-15739. [PMID: 32561643 PMCID: PMC7355028 DOI: 10.1073/pnas.2001989117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
De novo emergence demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can polypeptides confer functions of evolutionary relevance, and how might such polypeptides evolve into modern proteins? The earliest proteins present an even greater challenge, as they were likely based on abiotic, spontaneously synthesized amino acids. Here we asked whether a primordial function, such as nucleic acid binding, could emerge with ornithine, a basic amino acid that forms abiotically yet is absent in modern-day proteins. We combined ancestral sequence reconstruction and empiric deconstruction to unravel a gradual evolutionary trajectory leading from a polypeptide to a ubiquitous nucleic acid-binding protein. Intermediates along this trajectory comprise sequence-duplicated functional proteins built from 10 amino acid types, with ornithine as the only basic amino acid. Ornithine side chains were further modified into arginine by an abiotic chemical reaction, improving both structure and function. Along this trajectory, function evolved from phase separation with RNA (coacervates) to avid and specific double-stranded DNA binding. Our results suggest that phase-separating polypeptides may have been an evolutionary resource for the emergence of early proteins, and that ornithine, together with its postsynthesis modification to arginine, could have been the earliest basic amino acids.
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Affiliation(s)
- Liam M Longo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dragana Despotović
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orit Weil-Ktorza
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Fridmann-Sirkis
- Life Sciences Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Norman Metanis
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
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72
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Weitzner BD, Kipnis Y, Daniel AG, Hilvert D, Baker D. A computational method for design of connected catalytic networks in proteins. Protein Sci 2020; 28:2036-2041. [PMID: 31642127 PMCID: PMC6863703 DOI: 10.1002/pro.3757] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 02/05/2023]
Abstract
Computational design of new active sites has generally proceeded by geometrically defining interactions between the reaction transition state(s) and surrounding side‐chain functional groups which maximize transition‐state stabilization, and then searching for sites in protein scaffolds where the specified side‐chain–transition‐state interactions can be realized. A limitation of this approach is that the interactions between the side chains themselves are not constrained. An extensive connected hydrogen bond network involving the catalytic residues was observed in a designed retroaldolase following directed evolution. Such connected networks could increase catalytic activity by preorganizing active site residues in catalytically competent orientations, and enabling concerted interactions between side chains during catalysis, for example, proton shuffling. We developed a method for designing active sites in which the catalytic side chains, in addition to making interactions with the transition state, are also involved in extensive hydrogen bond networks. Because of the added constraint of hydrogen‐bond connectivity between the catalytic side chains, to find solutions, a wider range of interactions between these side chains and the transition state must be considered. Our new method starts from a ChemDraw‐like two‐dimensional representation of the transition state with hydrogen‐bond donors, acceptors, and covalent interaction sites indicated, and all placements of side‐chain functional groups that make the indicated interactions with the transition state, and are fully connected in a single hydrogen‐bond network are systematically enumerated. The RosettaMatch method can then be used to identify realizations of these fully‐connected active sites in protein scaffolds. The method generates many fully‐connected active site solutions for a set of model reactions that are promising starting points for the design of fully‐preorganized enzyme catalysts.
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Affiliation(s)
- Brian D Weitzner
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Yakov Kipnis
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - A Gerard Daniel
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
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73
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Ma C, Dong J, Viviani M, Tulini I, Pontillo N, Maity S, Zhou Y, Roos WH, Liu K, Herrmann A, Portale G. De novo rational design of a freestanding, supercharged polypeptide, proton-conducting membrane. SCIENCE ADVANCES 2020; 6:eabc0810. [PMID: 32832651 PMCID: PMC7439445 DOI: 10.1126/sciadv.abc0810] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/04/2020] [Indexed: 05/31/2023]
Abstract
Proton translocation enables important processes in nature and man-made technologies. However, controlling proton conduction and fabrication of devices exploiting biomaterials remains a challenge. Even more difficult is the design of protein-based bulk materials without any functional starting scaffold for further optimization. Here, we show the rational design of proton-conducting, protein materials exceeding reported proteinaceous systems. The carboxylic acid-rich structures were evolved step by step by exploring various sequences from intrinsically disordered coils over supercharged nanobarrels to hierarchically spider β sheet containing protein-supercharged polypeptide chimeras. The latter material is characterized by interconnected β sheet nanodomains decorated on their surface by carboxylic acid groups, forming self-supportive membranes and allowing for proton conduction in the hydrated state. The membranes showed an extraordinary proton conductivity of 18.5 ± 5 mS/cm at RH = 90%, one magnitude higher than other protein devices. This design paradigm offers great potential for bioprotonic device fabrication interfacing artificial and biological systems.
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Affiliation(s)
- Chao Ma
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jingjin Dong
- Macromolecular Chemistry and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Marco Viviani
- Macromolecular Chemistry and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Isotta Tulini
- Macromolecular Chemistry and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Nicola Pontillo
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Yu Zhou
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Wouter H. Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
- Department of Chemistry, Tsinghua University, 100084 Beijing, China
| | - Andreas Herrmann
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- DWI–Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Giuseppe Portale
- Macromolecular Chemistry and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
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74
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Himiyama T, Okamoto Y. Artificial Metalloenzymes: From Selective Chemical Transformations to Biochemical Applications. Molecules 2020; 25:molecules25132989. [PMID: 32629938 PMCID: PMC7411666 DOI: 10.3390/molecules25132989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 11/16/2022] Open
Abstract
Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: 1) the newly reported ArMs, according to their type of reaction, and 2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/in vivo catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan;
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Osaka 563-8577, Japan
| | - Yasunori Okamoto
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan
- Correspondence: ; Tel.: +81-22-795-5264
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75
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Affiliation(s)
- Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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76
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Learte‐Aymamí S, Vidal C, Gutiérrez‐González A, Mascareñas JL. Intracellular Reactions Promoted by Bis(histidine) Miniproteins Stapled Using Palladium(II) Complexes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Soraya Learte‐Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Cristian Vidal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Alejandro Gutiérrez‐González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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77
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Pinter TBJ, Koebke KJ, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds. Angew Chem Int Ed Engl 2020; 59:7678-7699. [PMID: 31441170 PMCID: PMC7035182 DOI: 10.1002/anie.201907502] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Indexed: 12/31/2022]
Abstract
The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
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78
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Pinter TBJ, Koebke KJ, Pecoraro VL. Katalyse und Elektronentransfer in helikalen De‐novo‐Gerüststrukturen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201907502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Vincent L. Pecoraro
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
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79
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Vornholt T, Jeschek M. The Quest for Xenobiotic Enzymes: From New Enzymes for Chemistry to a Novel Chemistry of Life. Chembiochem 2020; 21:2241-2249. [PMID: 32294286 DOI: 10.1002/cbic.202000121] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/13/2020] [Indexed: 12/19/2022]
Abstract
Enzyme engineering has made impressive progress in the past decades, paving the way for the widespread use of enzymes for various purposes. In contrast to "classical" enzyme engineering, which focuses on optimizing specific properties of natural enzymes, a more recent trend towards the creation of artificial enzymes that catalyze fundamentally distinct, new-to-nature reactions is observable. While approaches for creating such enzymes differ significantly, they share the common goal of enabling biocatalytic novelty to broaden the range of applications for enzymes. Although most artificial enzymes reported to date are only moderately active and barely function in vivo, they have the potential to endow cells with capabilities that were previously out of reach and thus herald a new wave of "functional xenobiology". Herein, we highlight recent developments in the field of artificial enzymes with a particular focus on challenges and opportunities for their use in xenobiology.
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Affiliation(s)
- Tobias Vornholt
- Department of Biosystems Science and Engineering ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Markus Jeschek
- Department of Biosystems Science and Engineering ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
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80
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Gardner JM, Biler M, Risso VA, Sanchez-Ruiz JM, Kamerlin SCL. Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00722] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jasmine M. Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Michal Biler
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A. Risso
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Shina C. L. Kamerlin
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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81
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Learte-Aymamí S, Vidal C, Gutiérrez-González A, Mascareñas JL. Intracellular Reactions Promoted by Bis(histidine) Miniproteins Stapled Using Palladium(II) Complexes. Angew Chem Int Ed Engl 2020; 59:9149-9154. [PMID: 32162393 DOI: 10.1002/anie.202002032] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Indexed: 12/24/2022]
Abstract
The generation of catalytically active metalloproteins inside living mammalian cells is a major research challenge at the interface between catalysis and cell biology. Herein we demonstrate that basic domains of bZIP transcription factors, mutated to include two histidine residues at i and i+4 positions, react with palladium(II) sources to generate catalytically active, stapled pallado-miniproteins. The resulting constrained peptides are efficiently internalized into living mammalian cells, where they perform palladium-promoted depropargylation reactions without cellular fixation. Control experiments confirm the requirement of the peptide scaffolding and the palladium staple for attaining the intracellular reactivity.
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Affiliation(s)
- Soraya Learte-Aymamí
- Centro Singular de Investigación en Química, Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Cristian Vidal
- Centro Singular de Investigación en Química, Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alejandro Gutiérrez-González
- Centro Singular de Investigación en Química, Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química, Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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82
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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83
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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84
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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85
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Abstract
While the bottom-up design of enzymes appears to be an intractably complex problem, a minimal approach that combines elementary, de novo-designed proteins with intrinsically reactive cofactors offers a simple means to rapidly access sophisticated catalytic mechanisms. Not only is this method proven in the reproduction of powerful oxidative chemistry of the natural peroxidase enzymes, but we show here that it extends to the efficient, abiological—and often asymmetric—formation of strained cyclopropane rings, nitrogen–carbon and carbon–carbon bonds, and the ring expansion of a simple cyclic molecule to form a precursor for NAD+, a fundamentally important biological cofactor. That the enzyme also functions in vivo paves the way for its incorporation into engineered biosynthetic pathways within living organisms. By constructing an in vivo-assembled, catalytically proficient peroxidase, C45, we have recently demonstrated the catalytic potential of simple, de novo-designed heme proteins. Here, we show that C45’s enzymatic activity extends to the efficient and stereoselective intermolecular transfer of carbenes to olefins, heterocycles, aldehydes, and amines. Not only is this a report of carbene transferase activity in a completely de novo protein, but also of enzyme-catalyzed ring expansion of aromatic heterocycles via carbene transfer by any enzyme.
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86
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Jeong WJ, Yu J, Song WJ. Proteins as diverse, efficient, and evolvable scaffolds for artificial metalloenzymes. Chem Commun (Camb) 2020; 56:9586-9599. [DOI: 10.1039/d0cc03137b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have extracted and categorized the desirable properties of proteins that are adapted as the scaffolds for artificial metalloenzymes.
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Affiliation(s)
- Woo Jae Jeong
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jaeseung Yu
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Woon Ju Song
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
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87
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Engineering Metalloprotein Functions in Designed and Native Scaffolds. Trends Biochem Sci 2019; 44:1022-1040. [DOI: 10.1016/j.tibs.2019.06.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
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88
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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]
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89
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Fischer J, Renn D, Quitterer F, Radhakrishnan A, Liu M, Makki A, Ghorpade S, Rueping M, Arold ST, Groll M, Eppinger J. Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Johannes Fischer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Dominik Renn
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | | | | | | | | | | - Stefan T. Arold
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
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90
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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91
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Towards functional de novo designed proteins. Curr Opin Chem Biol 2019; 52:102-111. [DOI: 10.1016/j.cbpa.2019.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/25/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
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92
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Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
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Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
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93
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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.
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94
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Burke AJ, Lovelock SL, Frese A, Crawshaw R, Ortmayer M, Dunstan M, Levy C, Green AP. Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Nature 2019; 570:219-223. [PMID: 31132786 DOI: 10.1038/s41586-019-1262-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/13/2019] [Indexed: 11/09/2022]
Abstract
The combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions1-4. However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis5, here we report the generation of a hydrolytic enzyme that uses Nδ-methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design6-10. Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free Nδ-methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. Nδ-methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine11, and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.
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Affiliation(s)
- Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Sarah L Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Amina Frese
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Rebecca Crawshaw
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Mary Ortmayer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Mark Dunstan
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Colin Levy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.
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95
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Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF. De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. Acc Chem Res 2019; 52:1148-1159. [PMID: 30973707 DOI: 10.1021/acs.accounts.8b00674] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
De novo protein design represents an attractive approach for testing and extending our understanding of metalloprotein structure and function. Here, we describe our work on the design of DF (Due Ferri or two-iron in Italian), a minimalist model for the active sites of much larger and more complex natural diiron and dimanganese proteins. In nature, diiron and dimanganese proteins protypically bind their ions in 4-Glu, 2-His environments, and they catalyze diverse reactions, ranging from hydrolysis, to O2-dependent chemistry, to decarbonylation of aldehydes. In the design of DF, the position of each atom-including the backbone, the first-shell ligands, the second-shell hydrogen-bonded groups, and the well-packed hydrophobic core-was bespoke using precise mathematical equations and chemical principles. The first member of the DF family was designed to be of minimal size and complexity and yet to display the quintessential elements required for binding the dimetal cofactor. After thoroughly characterizing its structural, dynamic, spectroscopic, and functional properties, we added additional complexity in a rational stepwise manner to achieve increasingly sophisticated catalytic functions, ultimately demonstrating substrate-gated four-electron reduction of O2 to water. We also briefly describe the extension of these studies to the design of proteins that bind nonbiological metal cofactors (a synthetic porphyrin and a tetranuclear cluster), and a Zn2+/proton antiporting membrane protein. Together these studies demonstrate a successful and generally applicable strategy for de novo metalloprotein design, which might indeed mimic the process by which primordial metalloproteins evolved. We began the design process with a highly symmetrical backbone and binding site, by using point-group symmetry to assemble the secondary structures that position the amino acid side chains required for binding. The resulting models provided a rough starting point and initial parameters for the subsequent precise design of the final protein using modern methods of computational protein design. Unless the desired site is itself symmetrical, this process requires reduction of the symmetry or lifting it altogether. Nevertheless, the initial symmetrical structure can be helpful to restrain the search space during assembly of the backbone. Finally, the methods described here should be generally applicable to the design of highly stable and robust catalysts and sensors. There is considerable potential in combining the efficiency and knowledge base associated with homogeneous metal catalysis with the programmability, biocompatibility, and versatility of proteins. While the work reported here focuses on testing and learning the principles of natural metalloproteins by designing and studying proteins one at a time, there is also considerable potential for using designed proteins that incorporate both biological and nonbiological metal ion cofactors for the evolution of novel catalysts.
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Affiliation(s)
- Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- IBB, National Research Council, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
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96
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Reetz MT. Directed Evolution of Artificial Metalloenzymes: A Universal Means to Tune the Selectivity of Transition Metal Catalysts? Acc Chem Res 2019; 52:336-344. [PMID: 30689339 DOI: 10.1021/acs.accounts.8b00582] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transition metal catalysts mediate a wide variety of chemo-, stereo-, and regioselective transformations, and therefore play a pivotal role in modern synthetic organic chemistry. Steric and electronic effects of ligands provide organic chemists with an exceedingly useful tool. More than four decades ago, chemists began to think about a different approach, namely, embedding achiral ligand/metal moieties covalently or noncovalently in protein hosts with formation of artificial metalloenzymes. While structurally fascinating, this approach led in each case only to a single (bio)catalyst, with its selectivity and activity being a matter of chance. In order to solve this fundamental problem, my group proposed in 2000-2002 the idea of directed evolution of artificial metalloenzymes. In earlier studies, we had already demonstrated that directed evolution of enzymes constitutes a viable method for enhancing and inverting the stereoselectivity of enzymes as catalysts in organic chemistry. We speculated that it should also be possible to manipulate selectivity and activity of artificial metalloenzymes, which would provide organic chemists with a tool for optimizing essentially any transition metal catalyzed reaction type. In order to put this vision into practice, we first turned to the Whitesides system for artificial metalloenzyme formation, comprising a biotinylated diphosphine/Rh moiety, which is anchored noncovalently to avidin or streptavidin. Following intensive optimization, proof of principle was finally demonstrated in 2006, which opened the door to a new research area. This personal Account critically assesses these early studies as well as subsequent efforts from my group focusing on different protein scaffolds, and includes briefly some of the most important current contributions of other groups. Two primary messages emerge: First, since organic chemists continue to be extremely good at designing and implementing man-made transition metal catalysts, often on a large scale, those scientists that are active in the equally intriguing field of directed evolution of artificial metalloenzymes should be moderate when generalizing claims. All factors required for a truly viable catalytic system need to be considered, especially activity and ease of upscaling. Second, the most exciting and thus far very rare cases of directed evolution of artificial metalloenzymes are those that focus on selective transformations that are not readily possible using state of the art transition metal catalysts.
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Affiliation(s)
- Manfred T. Reetz
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim Germany
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97
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Churchfield LA, Tezcan FA. Design and Construction of Functional Supramolecular Metalloprotein Assemblies. Acc Chem Res 2019; 52:345-355. [PMID: 30698941 DOI: 10.1021/acs.accounts.8b00617] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nature puts to use only a small fraction of metal ions in the periodic table. Yet, when incorporated into protein scaffolds, this limited set of metal ions carry out innumerable cellular functions and execute essential biochemical transformations such as photochemical H2O oxidation, O2 or CO2 reduction, and N2 fixation, highlighting the outsized importance of metalloproteins in biology. Not surprisingly, elucidating the intricate interplay between metal ions and protein structures has been the focus of extensive structural and mechanistic scrutiny over the last several decades. As a result of such top-down efforts, we have gained a reasonably detailed understanding of how metal ions shape protein structures and how protein structures in turn influence metal reactivity. It is fair to say that we now have some idea-and in some cases, a good idea-about how most known metalloproteins function and we possess enough insight to quickly assess the modus operandi of newly discovered ones. However, translating this knowledge into an ability to construct functional metalloproteins from scratch represents a challenge at a whole different level: it is one thing to know how an automobile works; it is another to build one. In our quest to build new metalloproteins, we have taken an original approach in which folded, monomeric proteins are used as ligands or synthons for building supramolecular complexes through metal-mediated self-assembly (MDPSA, Metal-Directed Protein Self-Assembly). The interfaces in the resulting protein superstructures are subsequently tailored with covalent, noncovalent, or additional metal-coordination interactions for stabilization and incorporation of new functionalities (MeTIR, Metal Templated Interface Redesign). In an earlier Account, we had described the proof-of-principle studies for MDPSA and MeTIR, using a four-helix bundle, heme protein cytochrome cb562 (cyt cb562), as a model building block. By the end of those studies, we were able to demonstrate that a tetrameric, Zn-directed cyt cb562 complex (Zn4:M14) could be stabilized through computationally prescribed noncovalent interactions inserted into the nascent protein-protein interfaces. In this Account, we first describe the rationale and motivation for our particular metalloprotein engineering strategy and a brief summary of our earlier work. We then describe the next steps in the "evolution" of bioinorganic complexity on the Zn4:M14 scaffold, namely, (a) the generation of a self-standing protein assembly that can stably and selectively bind metal ions, (b) the creation of reactive metal centers within the protein assembly, and (c) the coupling of metal coordination and reactivity to external stimuli through allosteric effects.
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Affiliation(s)
- Lewis A. Churchfield
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356, United States
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98
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Carvalho HF, Branco RJF, Leite FAS, Matzapetakis M, Roque ACA, Iranzo O. Hydrolytic zinc metallopeptides using a computational multi-state design approach. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01364d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combination of multi-state design and long-timescale conformational dynamics as a powerful strategy to obtain metalloenzymes.
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Affiliation(s)
- Henrique F. Carvalho
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Ricardo J. F. Branco
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Fábio A. S. Leite
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- 2780-157 Oeiras
- Portugal
| | - A. Cecília A. Roque
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
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99
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Clarke DE, Noguchi H, Gryspeerdt JLAG, De Feyter S, Voet ARD. Artificial β-propeller protein-based hydrolases. Chem Commun (Camb) 2019; 55:8880-8883. [DOI: 10.1039/c9cc04388h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We investigated symmetrical β-propeller protein scaffolds as artificial hydrolases and discovered their catalytic mechanism to be centred around a threonine–histidine dyad.
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Affiliation(s)
- David E. Clarke
- Division of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- Leuven
- Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | | | - Steven De Feyter
- Division of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- Leuven
- Belgium
| | - Arnout R. D. Voet
- Laboratory of Biomolecular Modelling and Design
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
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100
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Gutte B, Klauser S. Design of catalytic polypeptides and proteins. Protein Eng Des Sel 2018; 31:457-470. [PMID: 31241746 DOI: 10.1093/protein/gzz009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
The first part of this review article lists examples of complete, empirical de novo design that made important contributions to the development of the field and initiated challenging projects. The second part of this article deals with computational design of novel enzymes in native protein scaffolds; active designs were refined through random and site-directed mutagenesis producing artificial enzymes with nearly native enzyme- like activities against a number of non-natural substrates. Combining aspects of de novo design and biological evolution of nature's enzymes has started and will accelerate the development of novel enzyme activities.
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Affiliation(s)
- B Gutte
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - S Klauser
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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