1
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Almhjell PJ, Johnston KE, Porter NJ, Kennemur JL, Bhethanabotla VC, Ducharme J, Arnold FH. The β-subunit of tryptophan synthase is a latent tyrosine synthase. Nat Chem Biol 2024:10.1038/s41589-024-01619-z. [PMID: 38744987 DOI: 10.1038/s41589-024-01619-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
Aromatic amino acids and their derivatives are diverse primary and secondary metabolites with critical roles in protein synthesis, cell structure and integrity, defense and signaling. All de novo aromatic amino acid production relies on a set of ancient and highly conserved chemistries. Here we introduce a new enzymatic transformation for L-tyrosine synthesis by demonstrating that the β-subunit of tryptophan synthase-which natively couples indole and L-serine to form L-tryptophan-can act as a latent 'tyrosine synthase'. A single substitution of a near-universally conserved catalytic residue unlocks activity toward simple phenol analogs and yields exclusive para carbon-carbon bond formation to furnish L-tyrosines. Structural and mechanistic studies show how a new active-site water molecule orients phenols for a nonnative mechanism of alkylation, with additional directed evolution resulting in a net >30,000-fold rate enhancement. This new biocatalyst can be used to efficiently prepare valuable L-tyrosine analogs at gram scales and provides the missing chemistry for a conceptually different pathway to L-tyrosine.
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Affiliation(s)
- Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Kadina E Johnston
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Merck & Co., Inc, South San Francisco, CA, USA
| | - Nicholas J Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Codexis, Inc., Redwood City, CA, USA
| | - Jennifer L Kennemur
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vignesh C Bhethanabotla
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julie Ducharme
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Quebec Government Office, Los Angeles, CA, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Feid C, Luma L, Fischer T, Löffler JG, Grebenovsky N, Wachtveitl J, Heckel A, Bredenbeck J. Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer. Angew Chem Int Ed Engl 2024; 63:e202317047. [PMID: 38103205 DOI: 10.1002/anie.202317047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/18/2023]
Abstract
Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient. Here, we introduce two novel donor ncAAs based on an iminothioindoxyl (ITI) chromophore. The dimethylamino-ITI (DMA-ITI) and julolidine-ITI (J-ITI) moieties overcome the limitation of AzAla with a 50 times higher Vis extinction coefficient. While ITI moieties are known for ultrafast photoswitching, DMA-ITI and J-ITI exclusively form a hot ground state on the sub-ps timescale instead, which is essential for their usage as vibrational energy donor. In VET measurements of donor-sensor dipeptides we investigate the performance of the new donors. We observe 20 times larger signals compared to the established AzAla donor, which opens unprecedented possibilities for the study of VET in proteins.
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Affiliation(s)
- Carolin Feid
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Larita Luma
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
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3
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Villalona J, Higgins PM, Buller AR. Engineered Biocatalytic Synthesis of β-N-Substituted-α-Amino Acids. Angew Chem Int Ed Engl 2023; 62:e202311189. [PMID: 37625129 PMCID: PMC10592029 DOI: 10.1002/anie.202311189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 08/27/2023]
Abstract
Non-canonical amino acids (ncAAs) are useful synthons for the development of new medicines, materials, and probes for bioactivity. Recently, enzyme engineering has been leveraged to produce a suite of highly active enzymes for the synthesis of β-substituted amino acids. However, there are few examples of biocatalytic N-substitution reactions to make α,β-diamino acids. In this study, we used directed evolution to engineer the β-subunit of tryptophan synthase, TrpB, for improved activity with diverse amine nucleophiles. Mechanistic analysis shows that high yields are hindered by product re-entry into the catalytic cycle and subsequent decomposition. Additional equivalents of l-serine can inhibit product reentry through kinetic competition, facilitating preparative scale synthesis. We show β-substitution with a dozen aryl amine nucleophiles, including demonstration on a gram scale. These transformations yield an underexplored class of amino acids that can serve as unique building blocks for chemical biology and medicinal chemistry.
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Affiliation(s)
- Jairo Villalona
- Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Peyton M Higgins
- Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
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4
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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5
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022; 61:e202200648. [PMID: 35226765 PMCID: PMC9401566 DOI: 10.1002/anie.202200648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 11/10/2022]
Abstract
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
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Affiliation(s)
- Jan G. Löffler
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Erhan Deniz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Carolin Feid
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Valentin G. Franz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Jens Bredenbeck
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
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6
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan G. Löffler
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Erhan Deniz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Carolin Feid
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Valentin G. Franz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Jens Bredenbeck
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
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7
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Shatsauskas AL, Zablotskii YА, Chernenko SА, Zheleznova TY, Shuvalov VY, Kostyuchenko AS, Fisyuk AS. Synthesis and photophysical properties of the products of the reaction of 5-methyl-7-phenyl[1,3]oxazolo[5,4-b]pyridin-2(1H)-one with amino acids. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-021-03045-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8
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Ospina F, Schülke KH, Hammer SC. Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity. Chempluschem 2021; 87:e202100454. [PMID: 34821073 DOI: 10.1002/cplu.202100454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.
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Affiliation(s)
- Felipe Ospina
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kai H Schülke
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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9
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Watkins-Dulaney EJ, Dunham NP, Straathof S, Turi S, Arnold FH, Buller AR. Asymmetric Alkylation of Ketones Catalyzed by Engineered TrpB. Angew Chem Int Ed Engl 2021; 60:21412-21417. [PMID: 34269506 DOI: 10.1002/anie.202106938] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 11/12/2022]
Abstract
The β-subunit of tryptophan synthase (TrpB) catalyzes a PLP-mediated β-substitution reaction between indole and serine to form L-Trp. A succession of TrpB protein engineering campaigns to expand the enzyme's nucleophile substrate range has enabled the biocatalytic production of diverse non-canonical amino acids (ncAAs). Here, we show that ketone-derived enolates can serve as nucleophiles in the TrpB reaction to achieve the asymmetric alkylation of ketones, an outstanding challenge in synthetic chemistry. We engineered TrpB by directed evolution to catalyze the asymmetric alkylation of propiophenone and 2-fluoroacetophenone with a high degree of selectivity. In reactions with propiophenone, preference for the opposite product diastereomer emerges over the course of evolution, demonstrating that full control over the stereochemistry at the new chiral center can be achieved. The addition of this new reaction to the TrpB platform is a crucial first step toward the development of efficient methods to synthesize non-canonical prolines and other chirally dense nitrogen heterocycles.
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Affiliation(s)
- Ella J Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Noah P Dunham
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Soma Turi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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10
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Watkins‐Dulaney EJ, Dunham NP, Straathof S, Turi S, Arnold FH, Buller AR. Asymmetric Alkylation of Ketones Catalyzed by Engineered TrpB. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ella J. Watkins‐Dulaney
- Division of Biology and Biological Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Noah P. Dunham
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Soma Turi
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Andrew R. Buller
- Department of Chemistry University of Wisconsin—Madison 1101 University Avenue Madison WI 53706 USA
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11
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Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids. Nat Commun 2021; 12:3284. [PMID: 34078890 PMCID: PMC8172543 DOI: 10.1038/s41467-021-23591-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
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12
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Murfin LC, Lewis SE. Azulene-A Bright Core for Sensing and Imaging. Molecules 2021; 26:molecules26020353. [PMID: 33445502 PMCID: PMC7826776 DOI: 10.3390/molecules26020353] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Azulene is a hydrocarbon isomer of naphthalene known for its unusual colour and fluorescence properties. Through the harnessing of these properties, the literature has been enriched with a series of chemical sensors and dosimeters with distinct colorimetric and fluorescence responses. This review focuses specifically on the latter of these phenomena. The review is subdivided into two sections. Section one discusses turn-on fluorescent sensors employing azulene, for which the literature is dominated by examples of the unusual phenomenon of azulene protonation-dependent fluorescence. Section two focuses on fluorescent azulenes that have been used in the context of biological sensing and imaging. To aid the reader, the azulene skeleton is highlighted in blue in each compound.
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13
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Watkins-Dulaney E, Straathof S, Arnold F. Tryptophan Synthase: Biocatalyst Extraordinaire. Chembiochem 2021; 22:5-16. [PMID: 32677310 PMCID: PMC7935429 DOI: 10.1002/cbic.202000379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond-forming reaction between indole and serine to make l-tryptophan; native TrpS complexes possess fairly broad specificity for indole analogues, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteric regulation by its TrpA partner and has enabled dramatic expansion of the enzyme's substrate scope. This review examines the long and storied career of TrpS from the perspective of its application in ncAA synthesis and biocatalytic cascades.
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Affiliation(s)
- Ella Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Frances Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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14
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Pluchinsky AJ, Wackelin DJ, Huang X, Arnold FH, Mrksich M. High Throughput Screening with SAMDI Mass Spectrometry for Directed Evolution. J Am Chem Soc 2020; 142:19804-19808. [PMID: 33174742 DOI: 10.1021/jacs.0c07828] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Advances in directed evolution have led to an exploration of new and important chemical transformations; however, many of these efforts still rely on the use of low-throughput chromatography-based screening methods. We present a high-throughput strategy for screening libraries of enzyme variants for improved activity. Unpurified reaction products are immobilized to a self-assembled monolayer and analyzed by mass spectrometry, allowing for direct evaluation of thousands of variants in under an hour. The method was demonstrated with libraries of randomly mutated cytochrome P411 variants to identify improved catalysts for C-H alkylation. The technique may be tailored to evolve enzymatic activity for a variety of transformations where higher throughput is needed.
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Affiliation(s)
| | - Daniel J Wackelin
- Division of Chemistry and Chemical Engineering MC 210-41, California Institute of Technology, Pasadena, California 91125, United States
| | - Xiongyi Huang
- Division of Chemistry and Chemical Engineering MC 210-41, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering MC 210-41, California Institute of Technology, Pasadena, California 91125, United States
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15
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Rix G, Watkins-Dulaney EJ, Almhjell PJ, Boville CE, Arnold FH, Liu CC. Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. Nat Commun 2020; 11:5644. [PMID: 33159067 PMCID: PMC7648111 DOI: 10.1038/s41467-020-19539-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/19/2020] [Indexed: 01/11/2023] Open
Abstract
Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolve the Thermotoga maritima tryptophan synthase β-subunit (TmTrpB) through multi-mutation pathways in many independent replicates, selecting only on TmTrpB's primary activity of synthesizing L-tryptophan from indole and L-serine. We find that the resulting sequence-diverse TmTrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of biomolecular functions.
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Affiliation(s)
- Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Ella J Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christina E Boville
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aralez Bio, Emeryville, CA, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chang C Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
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16
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Gupta A, Garreffi BP, Guo M. Facile synthesis of a novel genetically encodable fluorescent α-amino acid emitting greenish blue light. Chem Commun (Camb) 2020; 56:12578-12581. [PMID: 32944728 PMCID: PMC7577945 DOI: 10.1039/d0cc03643a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report the facile synthesis and characterization of a novel fluorescent α-amino acid 4-phenanthracen-9-yl-l-phenylalanine (Phen-AA) (5) that emits greenish blue light in the visible region. This genetically encodable l-α-amino acid has excellent photostability with a 75% quantum yield. It readily gets into human cells, being clearly imaged upon 405 nm laser excitation. The synthetic procedure is resistant to racemization and only involves three simple steps which use mild conditions and generate the Phen-AA in reasonably good yield. It may find broad applications in research, biotechnology, and the pharmaceutical industry.
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Affiliation(s)
- Aakash Gupta
- Department of Chemistry and Biochemistry, UMass Cranberry Health Research Center, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA.
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Martínez-Rodríguez S, Torres JM, Sánchez P, Ortega E. Overview on Multienzymatic Cascades for the Production of Non-canonical α-Amino Acids. Front Bioeng Biotechnol 2020; 8:887. [PMID: 32850740 PMCID: PMC7431475 DOI: 10.3389/fbioe.2020.00887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The 22 genetically encoded amino acids (AAs) present in proteins (the 20 standard AAs together with selenocysteine and pyrrolysine), are commonly referred as proteinogenic AAs in the literature due to their appearance in ribosome-synthetized polypeptides. Beyond the borders of this key set of compounds, the rest of AAs are generally named imprecisely as non-proteinogenic AAs, even when they can also appear in polypeptide chains as a result of post-transductional machinery. Besides their importance as metabolites in life, many of D-α- and L-α-"non-canonical" amino acids (NcAAs) are of interest in the biotechnological and biomedical fields. They have found numerous applications in the discovery of new medicines and antibiotics, drug synthesis, cosmetic, and nutritional compounds, or in the improvement of protein and peptide pharmaceuticals. In addition to the numerous studies dealing with the asymmetric synthesis of NcAAs, many different enzymatic pathways have been reported in the literature allowing for the biosynthesis of NcAAs. Due to the huge heterogeneity of this group of molecules, this review is devoted to provide an overview on different established multienzymatic cascades for the production of non-canonical D-α- and L-α-AAs, supplying neophyte and experienced professionals in this field with different illustrative examples in the literature. Whereas the discovery of new or newly designed enzymes is of great interest, dusting off previous enzymatic methodologies by a "back and to the future" strategy might accelerate the implementation of new or improved multienzymatic cascades.
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