1
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Kuru E, Rittichier J, de Puig H, Flores A, Rout S, Han I, Reese AE, Bartlett TM, De Moliner F, Bernier SG, Galpin JD, Marchand J, Bedell W, Robinson-McCarthy L, Ahern CA, Bernhardt TG, Rudner DZ, Collins JJ, Vendrell M, Church GM. Rapid discovery and evolution of nanosensors containing fluorogenic amino acids. Nat Commun 2024; 15:7531. [PMID: 39237489 PMCID: PMC11377706 DOI: 10.1038/s41467-024-50956-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/24/2024] [Indexed: 09/07/2024] Open
Abstract
Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.
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Affiliation(s)
- Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - Jonathan Rittichier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- EnPlusOne Biosciences Inc., Watertown, MA, USA
| | - Helena de Puig
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Allison Flores
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Subhrajit Rout
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Isaac Han
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Abigail E Reese
- IRR Chemistry Hub and Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Thomas M Bartlett
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Fabio De Moliner
- IRR Chemistry Hub and Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Sylvie G Bernier
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Jorge Marchand
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - William Bedell
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Marc Vendrell
- IRR Chemistry Hub and Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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3
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Zhu HX, Wright BW, Logel DY, Needham P, Yehl K, Molloy MP, Jaschke PR. IbpAB small heat shock proteins are not host factors for bacteriophage ϕX174 replication. Virology 2024; 597:110169. [PMID: 38996611 DOI: 10.1016/j.virol.2024.110169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Bacteriophage ϕX174 is a small icosahedral virus of the Microviridae with a rapid replication cycle. Previously, we found that in ϕX174 infections of Escherichia coli, the most highly upregulated host proteins are two small heat shock proteins, IbpA and IbpB, belonging to the HSP20 family, which is a universally conserved group of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Heat shock proteins were found to protect against ϕX174 lysis, but IbpA/B have not been studied. In this work, we disrupted the ibpA and ibpB genes and measured the effects on ϕX174 replication. We found that in contrast to other E. coli heat shock proteins, they are not necessary for ϕX174 replication; moreover, their absence has no discernible effect on ϕX174 fecundity. These results suggest IbpA/B upregulation is a response to ϕX174 protein expression but does not play a role in phage replication, and they are not Microviridae host factors.
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Affiliation(s)
- Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bradley W Wright
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Patrick Needham
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Kevin Yehl
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Mark P Molloy
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; Kolling Institute, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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4
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Hupfeld E, Schlee S, Wurm JP, Rajendran C, Yehorova D, Vos E, Ravindra Raju D, Kamerlin SCL, Sprangers R, Sterner R. Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα) 8-Barrel Enzyme of Histidine Biosynthesis HisF. JACS AU 2024; 4:3258-3276. [PMID: 39211614 PMCID: PMC11350729 DOI: 10.1021/jacsau.4c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The overall significance of loop motions for enzymatic activity is generally accepted. However, it has largely remained unclear whether and how such motions can control different steps of catalysis. We have studied this problem on the example of the mobile active site β1α1-loop (loop1) of the (βα)8-barrel enzyme HisF, which is the cyclase subunit of imidazole glycerol phosphate synthase. Loop1 variants containing single mutations of conserved amino acids showed drastically reduced rates for the turnover of the substrates N'-[(5'-phosphoribulosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) and ammonia to the products imidazole glycerol phosphate (ImGP) and 5-aminoimidazole-4-carboxamide-ribotide (AICAR). A comprehensive mechanistic analysis including stopped-flow kinetics, X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations detected three conformations of loop1 (open, detached, closed) whose populations differed between wild-type HisF and functionally affected loop1 variants. Transient stopped-flow kinetic experiments demonstrated that wt-HisF binds PrFAR by an induced-fit mechanism whereas catalytically impaired loop1 variants bind PrFAR by a simple two-state mechanism. Our findings suggest that PrFAR-induced formation of the closed conformation of loop1 brings active site residues in a productive orientation for chemical turnover, which we show to be the rate-limiting step of HisF catalysis. After the cyclase reaction, the closed loop conformation is destabilized, which favors the formation of detached and open conformations and hence facilitates the release of the products ImGP and AICAR. Our data demonstrate how different conformations of active site loops contribute to different catalytic steps, a finding that is presumably of broad relevance for the reaction mechanisms of (βα)8-barrel enzymes and beyond.
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Affiliation(s)
- Enrico Hupfeld
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Sandra Schlee
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Dariia Yehorova
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Eva Vos
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Dinesh Ravindra Raju
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Shina Caroline Lynn Kamerlin
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Remco Sprangers
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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5
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Yi S, Kim D, Cho W, Lee JH, Kwon JH, Kim J, Park SB. Rational Design of Pyrido[3,2- b]indolizine as a Tunable Fluorescent Scaffold for Fluorogenic Bioimaging. JACS AU 2024; 4:2896-2906. [PMID: 39211616 PMCID: PMC11350592 DOI: 10.1021/jacsau.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 09/04/2024]
Abstract
Novel fluorescent scaffolds are highly demanding for a wide range of applications in biomedical investigation. To meet this demand, the pyrido[3,2-b]indolizine scaffold was designed as a versatile organic fluorophore. With the aid of computational modeling, fluorophores offering tunable emission colors (blue to red) were constructed. Notably, constructed fluorophores absorb lights in the visible range (>400 nm) despite their small sizes (<300 g/mol). Among the fluorophores was discovered a highly fluorogenic fluorophore with a unique turn-on property, 1, and it was developed into a washing-free bioprobe for visualizing cellular lipid droplets in living cells. Furthermore, motivated by the core's compact size and structural analogy to indole, unprecedented tryptophan-analogous fluorogenic unnatural amino acids were constructed and incorporated into fluorogenic peptide probes for monitoring peptide-protein interactions.
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Affiliation(s)
- Sihyeong Yi
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Dahham Kim
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Wansang Cho
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jung Ho Lee
- Department
of Biophysics and Chemical Biology, Seoul
National University, Seoul 08826, Korea
| | - Ji Hoon Kwon
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jonghoon Kim
- Department
of Chemistry and Integrative Institute of Basic Science, Department
of Green Chemistry and Materials Engineering, Soongsil University, Seoul 06978, Korea
| | - Seung Bum Park
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Department
of Biophysics and Chemical Biology, Seoul
National University, Seoul 08826, Korea
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6
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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7
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Söllner J, Derler I. Genetic code expansion, an emerging tool in the Ca 2+ ion channel field. J Physiol 2024; 602:3297-3313. [PMID: 38695316 DOI: 10.1113/jp285840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 07/17/2024] Open
Abstract
Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.
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Affiliation(s)
- Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
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8
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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9
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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10
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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11
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Reese A, de Moliner F, Mendive-Tapia L, Benson S, Kuru E, Bridge T, Richards J, Rittichier J, Kitamura T, Sachdeva A, McSorley HJ, Vendrell M. Inserting "OFF-to-ON" BODIPY Tags into Cytokines: A Fluorogenic Interleukin IL-33 for Real-Time Imaging of Immune Cells. ACS CENTRAL SCIENCE 2024; 10:143-154. [PMID: 38292608 PMCID: PMC10823590 DOI: 10.1021/acscentsci.3c01125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 02/01/2024]
Abstract
The essential functions that cytokine/immune cell interactions play in tissue homeostasis and during disease have prompted the molecular design of targeted fluorophores to monitor their activity in real time. Whereas activatable probes for imaging immune-related enzymes are common, many immunological functions are mediated by binding events between cytokines and their cognate receptors that are hard to monitor by live-cell imaging. A prime example is interleukin-33 (IL-33), a key cytokine in innate and adaptive immunity, whose interaction with the ST2 cell-surface receptor results in downstream signaling and activation of NF-κB and AP-1 pathways. In the present work, we have designed a chemical platform to site-specifically introduce OFF-to-ON BODIPY fluorophores into full cytokine proteins and generate the first nativelike fluorescent analogues of IL-33. Among different incorporation strategies, chemical aminoacylation followed by bioorthogonal derivatization led to the best labeling results. Importantly, the BODIPY-labeled IL-33 derivatives-unlike IL-33-GFP constructs-exhibited ST2-specific binding and downstream bioactivity profiles comparable to those of the wild-type interleukin. Real-time fluorescence microscopy assays under no wash conditions confirmed the internalization of IL-33 through ST2 receptors and its intracellular trafficking through the endosomal pathway. We envision that the modularity and versatility of our BODIPY labeling platform will facilitate the synthesis of minimally tagged fluorogenic cytokines as the next generation of imaging reagents for real-time visualization of signaling events in live immune cells.
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Affiliation(s)
- Abigail
E. Reese
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Fabio de Moliner
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Lorena Mendive-Tapia
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Sam Benson
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Erkin Kuru
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
| | - Thomas Bridge
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Josh Richards
- Division
of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Jonathan Rittichier
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Takanori Kitamura
- Centre
for Reproductive Health, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
| | - Amit Sachdeva
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Henry J. McSorley
- Division
of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Marc Vendrell
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
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12
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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [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: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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13
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Brown W, Wesalo J, Samanta S, Luo J, Caldwell SE, Tsang M, Deiters A. Genetically Encoded Aminocoumarin Lysine for Optical Control of Protein-Nucleotide Interactions in Zebrafish Embryos. ACS Chem Biol 2023; 18:1305-1314. [PMID: 37272594 PMCID: PMC10278064 DOI: 10.1021/acschembio.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023]
Abstract
The strategic placement of unnatural amino acids into the active site of kinases and phosphatases has allowed for the generation of photocaged signaling proteins that offer spatiotemporal control over activation of these pathways through precise light exposure. However, deploying this technology to study cell signaling in the context of embryo development has been limited. The promise of optical control is especially useful in the early stages of an embryo where development is driven by tightly orchestrated signaling events. Here, we demonstrate light-induced activation of Protein Kinase A and a RASopathy mutant of NRAS in the zebrafish embryo using a new light-activated amino acid. We applied this approach to gain insight into the roles of these proteins in gastrulation and heart development and forge a path for further investigation of RASopathy mutant proteins in animals.
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Affiliation(s)
- Wes Brown
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Subhas Samanta
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ji Luo
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Steven E. Caldwell
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department
of Developmental Biology, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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14
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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15
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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16
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Li M, Peng T. Genetic Encoding of a Fluorescent Noncanonical Amino Acid as a FRET Donor for the Analysis of Deubiquitinase Activities. Methods Mol Biol 2023; 2676:55-67. [PMID: 37277624 DOI: 10.1007/978-1-0716-3251-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The genetic code expansion technology enables the genetic encoding of fluorescent noncanonical amino acids (ncAAs) for site-specific fluorescent labeling of proteins. These co-translational and internal fluorescent tags have been harnessed to establish genetically encoded Förster resonance energy transfer (FRET) probes for studying protein structural changes and interactions. Here, we describe the protocols for site-specific incorporation of an aminocoumarin-derived fluorescent ncAA into proteins in E. coli and preparation of a fluorescent ncAA-based FRET probe for assaying the activities of deubiquitinases, a key class of enzymes involved in ubiquitination. We also describe the deployment of an in vitro fluorescence assay to screen and analyze small-molecule inhibitors against deubiquitinases.
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Affiliation(s)
- Manjia Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
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17
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Duan HZ, Hu C, Li YL, Wang SH, Xia Y, Liu X, Wang J, Chen YX. Genetically Encoded Phosphine Ligand for Metalloprotein Design. J Am Chem Soc 2022; 144:22831-22837. [DOI: 10.1021/jacs.2c09683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Hua-Zhen Duan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Cheng Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Yue-Lin Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Shi-Hao Wang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yan Xia
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
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18
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Li M, Wang F, Yan L, Lu M, Zhang Y, Peng T. Genetically encoded fluorescent unnatural amino acids and FRET probes for detecting deubiquitinase activities. Chem Commun (Camb) 2022; 58:10186-10189. [PMID: 36000311 DOI: 10.1039/d2cc03623a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we present the genetic encoding of 7-aminocoumarin-based lysine derivatives, ACouK and AFCouK, into proteins in both bacterial and mammalian cells and the characterization of FRET pairs comprising ACouK or AFCouK as the donor and GFP as the acceptor. We further report the application of the FRET pairs to construct fully genetically encoded ratiometric probes for detecting deubiquitinases and screening for inhibitors.
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Affiliation(s)
- Manjia Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Feifei Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Long Yan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Minghao Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Yuqing Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China. .,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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19
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Benson S, de Moliner F, Tipping W, Vendrell M. Miniaturized Chemical Tags for Optical Imaging. Angew Chem Int Ed Engl 2022; 61:e202204788. [PMID: 35704518 PMCID: PMC9542129 DOI: 10.1002/anie.202204788] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/06/2022]
Abstract
Recent advances in optical bioimaging have prompted the need for minimal chemical reporters that can retain the molecular recognition properties and activity profiles of biomolecules. As a result, several methodologies to reduce the size of fluorescent and Raman labels to a few atoms (e.g., single aryl fluorophores, Raman-active triple bonds and isotopes) and embed them into building blocks (e.g., amino acids, nucleobases, sugars) to construct native-like supramolecular structures have been described. The integration of small optical reporters into biomolecules has also led to smart molecular entities that were previously inaccessible in an expedite manner. In this article, we review recent chemical approaches to synthesize miniaturized optical tags as well as some of their multiple applications in biological imaging.
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Affiliation(s)
- Sam Benson
- Centre for Inflammation ResearchThe University of EdinburghEdinburghEH16 4TJUK
| | - Fabio de Moliner
- Centre for Inflammation ResearchThe University of EdinburghEdinburghEH16 4TJUK
| | - William Tipping
- Centre for Molecular NanometrologyThe University of StrathclydeGlasgowG1 1RDUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEdinburghEH16 4TJUK
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20
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Ma X, Wei B, Wang E. Efficient incorporation of p-azido-l-phenylalanine into the protein using organic solvents. Protein Expr Purif 2022; 200:106158. [PMID: 36007861 DOI: 10.1016/j.pep.2022.106158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022]
Abstract
Azide, the most used photo-crosslinking group, facilitates the analysis of protein structure and function. This group is particularly useful when photochemically label antibodies and examine protein-protein interactions. The use of the expanded genetic code technique allows the special labeling of the functional azide group in proteins by adding the unnatural amino acid (UAA), p-azido-l-phenylalanine (AzF), in response to the amber codon during translation. However, a low UAA uptake rate due to mass transfer resistance in the cell membrane may lead to the early termination of the full-length protein. This study reports a general method for the efficient in vivo incorporation of AzF into the target protein by improving cell permeability using organic solvents. As expected, the yield of the full-length protein was significantly increased, which indicated that the AzF uptake was greatly improved due to the addition of organic solvents. Our method can serve as a good reference for improving the genetic incorporation of other kinds of UAAs into proteins.
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Affiliation(s)
- Xiaofeng Ma
- Department of Gynecology and Obstetrics, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230601, China
| | - Bing Wei
- Department of Gynecology and Obstetrics, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230601, China
| | - Enlin Wang
- The College of Life Science, Nankai University, Tianjin, 300071, China.
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21
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Wang P, Zhang G, Xu Z, Chen Z, Liu X, Wang C, Zheng C, Wang J, Zhang H, Yan A. Whole-cell FRET monitoring of transcription factor activities enables functional annotation of signal transduction systems in living bacteria. J Biol Chem 2022; 298:102258. [PMID: 35839853 PMCID: PMC9396075 DOI: 10.1016/j.jbc.2022.102258] [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: 02/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria adapt to their constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor TF–promoter interactions in situ in living bacteria are lacking. Herein, we developed a whole-cell TF–promoter binding assay based on the intermolecular FRET between an unnatural amino acid, l-(7-hydroxycoumarin-4-yl) ethylglycine, which labels TFs with bright fluorescence through genetic encoding (donor fluorophore) and the live cell nucleic acid stain SYTO 9 (acceptor fluorophore). We show that this new FRET pair monitors the intricate TF–promoter interactions elicited by various types of signal transduction systems, including one-component (CueR) and two-component systems (BasSR and PhoPQ), in bacteria with high specificity and sensitivity. We demonstrate that robust CouA incorporation and FRET occurrence is achieved in all these regulatory systems based on either the crystal structures of TFs or their simulated structures, if 3D structures of the TFs were unavailable. Furthermore, using CueR and PhoPQ systems as models, we demonstrate that the whole-cell FRET assay is applicable for the identification and validation of complex regulatory circuit and novel modulators of regulatory systems of interest. Finally, we show that the FRET system is applicable for single-cell analysis and monitoring TF activities in Escherichia coli colonizing a Caenorhabditis elegans host. In conclusion, we established a tractable and sensitive TF–promoter binding assay, which not only complements currently available approaches for DNA–protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria–host interface.
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Affiliation(s)
- Pengchao Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Guangming Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zhe Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Chenyin Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 15 Datun Road, Chaoyang District, Beijing 100101, China.
| | - Hongmin Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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22
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Benson S, de Moliner F, Tipping W, Vendrell M. Miniaturized Chemical Tags for Optical Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sam Benson
- The University of Edinburgh Centre for Inflammation Research UNITED KINGDOM
| | - Fabio de Moliner
- The University of Edinburgh Centre for Inflammation Research UNITED KINGDOM
| | - William Tipping
- University of Strathclyde Centre for Molecular Nanometrology UNITED KINGDOM
| | - Marc Vendrell
- University of Edinburgh Centre for Inflammation Research 47 Little France Crescent EH16 4TJ Edinburgh UNITED KINGDOM
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23
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Mala P, Saraogi I. Enhanced Codon-Anticodon Interaction at In-Frame UAG Stop Codon Improves the Efficiency of Non-Natural Amino Acid Mutagenesis. ACS Chem Biol 2022; 17:1051-1060. [PMID: 35532803 DOI: 10.1021/acschembio.1c00782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The introduction of non-natural amino acids into proteins through the stop codon readthrough methodology has been used to design proteins for diverse applications. However, this method suffers from low yields of the modified protein, as the suppressor tRNA that recognizes the stop codon is unable to compete effectively with release factor 1 (RF1), which terminates translation. We reasoned that a suppressor tRNA with improved interaction with the UAG stop codon on the mRNA will be able to compete more effectively with RF1. To test this idea, we inserted two 2,6-diaminopurine (D) units in the tRNA anticodon stem loop, including one at the third position of the tRNA anticodon. The modified suppressor tRNA could potentially form additional H-bonds between the N2-exocyclic amine of D and the C2 carbonyl group of uracil, thereby enhancing mRNA-tRNA interaction and/or altering tRNA conformation. The stronger interaction at the codon-anticodon interface resulted in improved UAG decoding efficiency and a higher yield of the modified protein containing a non-natural amino acid at multiple sites. Our findings are consistent with the importance of hydrogen bonding and tRNA conformation at the tRNA-mRNA duplex interface during in-frame UAG suppression, which improves protein translation at multiple UAG stop sites. This work provides valuable inputs toward improved non-natural amino acid mutagenesis for creating designer proteins.
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Affiliation(s)
- Purnima Mala
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
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24
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Heiss TK, Dorn RS, Ferreira AJ, Love AC, Prescher JA. Fluorogenic Cyclopropenones for Multicomponent, Real-Time Imaging. J Am Chem Soc 2022; 144:7871-7880. [PMID: 35442034 PMCID: PMC9377832 DOI: 10.1021/jacs.2c02058] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorogenic bioorthogonal reactions enable biomolecule visualization in real time. These reactions comprise reporters that "light up" upon reaction with complementary partners. While the spectrum of fluorogenic chemistries is expanding, few transformations are compatible with live cells due to cross-reactivities or insufficient signal turn-on. To address the need for more suitable chemistries for cellular imaging, we developed a fluorogenic reaction featuring cyclopropenone reporters and phosphines. The transformation involves regioselective activation and cyclization of cyclopropenones to form coumarin products. With optimal probes, the reaction provides >1600-fold signal turn-on, one of the highest fluorescence enhancements reported to date. The bioorthogonal motifs were evaluated in vitro and in cells. The reaction was also found to be compatible with other common fluorogenic transformations, enabling multicomponent, real-time imaging. Collectively, these data suggest that the cyclopropenone-phosphine reaction will bolster efforts to track biomolecule targets in their native settings.
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Affiliation(s)
- Tyler K Heiss
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Robert S Dorn
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Andrew J Ferreira
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Anna C Love
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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25
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Mendive‐Tapia L, Mendive‐Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Rationales Design von Phe-BODIPY-Aminosäuren als fluorogene Bausteine für den peptidbasierten Nachweis von Candida-Infektionen im Harntrakt. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202117218. [PMID: 38505242 PMCID: PMC10946803 DOI: 10.1002/ange.202117218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/08/2022]
Abstract
AbstractPilzinfektionen, die durch Candida‐Arten verursacht werden, gehören zu den häufigsten Infektionen bei Krankenhauspatienten. Die derzeitigen Methoden zum Nachweis von Candida‐Pilzzellen in klinischen Proben beruhen jedoch auf zeitaufwändigen Analysen, die eine schnelle und zuverlässige Diagnose erschweren. In diesem Beitrag beschreiben wir die rationale Entwicklung neuer Phe‐BODIPY‐Aminosäuren als kleine fluorogene Bausteine und ihre Anwendung zur Erzeugung fluoreszierender antimikrobieller Peptide für die schnelle Markierung von Candida‐Zellen im Urin. Mit Hilfe von computergestützten Berechnungen haben wir das fluorogene Verhalten von BODIPY‐substituierten aromatischen Aminosäuren analysiert und Bioaktivitäts‐ und konfokale Mikroskopieexperimente bei verschiedenen Stämmen durchgeführt, um den Nutzen und die Vielseitigkeit von Peptiden mit Phe‐BODIPYs zu bestätigen. Schließlich haben wir einen einfachen und sensitiven fluoreszensbasierten Test zum Nachweis von Candida albicans in menschlichen Urinproben entwickelt.
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Affiliation(s)
- Lorena Mendive‐Tapia
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - David Mendive‐Tapia
- Abteilung Theoretische ChemiePhysikalisch-Chemisches InstitutUniversität Heidelberg69120HeidelbergDeutschland
| | - Can Zhao
- Manchester Fungal Infection GroupAbteilung für EvolutionInfektion und GenomikM139NTManchesterGroßbritannien
| | - Doireann Gordon
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - Sam Benson
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - Michael J. Bromley
- Manchester Fungal Infection GroupAbteilung für EvolutionInfektion und GenomikM139NTManchesterGroßbritannien
| | - Wei Wang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Jun Wu
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Adelina Kopp
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Marc Vendrell
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
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Mendive‐Tapia L, Mendive‐Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Rational Design of Phe-BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide-Based Detection of Urinary Tract Candida Infections. Angew Chem Int Ed Engl 2022; 61:e202117218. [PMID: 35075763 PMCID: PMC9305947 DOI: 10.1002/anie.202117218] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 12/11/2022]
Abstract
Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time-consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe-BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY-substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe-BODIPYs. Finally, we have designed a simple and sensitive fluorescence-based assay for the detection of Candida albicans in human urine samples.
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Affiliation(s)
| | - David Mendive‐Tapia
- Department Theoretische ChemiePhysikalisch-Chemisches InstitutUniversität Heidelberg69120HeidelbergGermany
| | - Can Zhao
- Manchester Fungal Infection GroupDivision of EvolutionInfection and GenomicsUniversity of ManchesterM139NTManchesterUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Sam Benson
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Michael J. Bromley
- Manchester Fungal Infection GroupDivision of EvolutionInfection and GenomicsUniversity of ManchesterM139NTManchesterUK
| | - Wei Wang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Jun Wu
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Adelina Kopp
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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27
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Energy-based fragmentation contribution approach for calculating the fluorescence spectrum of biomacromolecules. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Yang K, Yu M, Zhu X, Xia Y, Li F, Li Y, Liu X, Wang J. Genetic Incorporation of Fluorescent Amino Acid into Fatty Acid Binding Protein for Fatty Acid Detection. J Mol Biol 2022; 434:167498. [DOI: 10.1016/j.jmb.2022.167498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 01/13/2023]
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29
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Structural basis for blocked excited state proton transfer in a fluorescent, photoacidic non-canonical amino acid-containing antibody fragment. J Mol Biol 2022; 434:167455. [PMID: 35033559 PMCID: PMC9018508 DOI: 10.1016/j.jmb.2022.167455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/05/2022] [Accepted: 01/09/2022] [Indexed: 11/20/2022]
Abstract
The fluorescent non-canonical amino acid (fNCAA) L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) contains a photoacidic 7-hydroxycoumarin (7-HC) side chain whose fluorescence properties can be tuned by its environment. In proteins, many alterations to 7-HCAA's fluorescence spectra have been reported including increases and decreases in intensity and red- and blue-shifted emission maxima. The ability to rationally design protein environments that alter 7-HCAA's fluorescence properties in predictable ways could lead to novel protein-based sensors of biological function. However, these efforts are likely limited by a lack of structural characterization of 7-HCAA-containing proteins. Here, we report the steady-state spectroscopic and x-ray crystallographic characterization of a 7-HCAA-containing antibody fragment (in the apo and antigen-bound forms) in which a substantially blue-shifted 7-HCAA emission maximum (∼70 nm) is observed relative to the free amino acid. Our structural characterization of these proteins provides evidence that the blue shift is a consequence of the fact that excited state proton transfer (ESPT) from the 7-HC phenol has been almost completely blocked by interactions with the protein backbone. Furthermore, a direct interaction between a residue in the antigen and the fluorophore served to further block proton transfer relative to the apoprotein. The structural basis of the unprecedented blue shift in 7-HCAA emission reported here provides a framework for the development of new fluorescent protein-based sensors.
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30
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Aphicho K, Kittipanukul N, Uttamapinant C. Visualizing the complexity of proteins in living cells with genetic code expansion. Curr Opin Chem Biol 2022; 66:102108. [PMID: 35026612 DOI: 10.1016/j.cbpa.2021.102108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Genetic code expansion has emerged as an enabling tool to provide insight into functions of understudied proteinogenic species, such as small proteins and peptides, and to probe protein biophysics in the cellular context. Here, we discuss recent technical advances and applications of genetic code expansion in cellular imaging of complex mammalian protein species, along with considerations and challenges on using the method.
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Affiliation(s)
- Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Narongyot Kittipanukul
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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31
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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32
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Kim S, Yi H, Kim YT, Lee HS. Engineering Translation Components for Genetic Code Expansion. J Mol Biol 2021; 434:167302. [PMID: 34673113 DOI: 10.1016/j.jmb.2021.167302] [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: 07/29/2021] [Revised: 09/26/2021] [Accepted: 10/05/2021] [Indexed: 12/18/2022]
Abstract
The expansion of the genetic code consisting of four bases and 20 amino acids into diverse building blocks has been an exciting topic in synthetic biology. Many biochemical components are involved in gene expression; therefore, adding a new component to the genetic code requires engineering many other components that interact with it. Genetic code expansion has advanced significantly for the last two decades with the engineering of several components involved in protein synthesis. These components include tRNA/aminoacyl-tRNA synthetase, new codons, ribosomes, and elongation factor Tu. In addition, biosynthesis and enhanced uptake of non-canonical amino acids have been attempted and have made meaningful progress. This review discusses the efforts to engineer these translation components, to improve the genetic code expansion technology.
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Affiliation(s)
- Sooin Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Hanbin Yi
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Yurie T Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea.
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33
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Jones CM, Robkis DM, Blizzard RJ, Munari M, Venkatesh Y, Mihaila TS, Eddins AJ, Mehl RA, Zagotta WN, Gordon SE, Petersson EJ. Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells. Chem Sci 2021; 12:11955-11964. [PMID: 34976337 PMCID: PMC8634729 DOI: 10.1039/d1sc01914g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/18/2021] [Indexed: 01/28/2023] Open
Abstract
Acridonylalanine (Acd) is a fluorescent amino acid that is highly photostable, with a high quantum yield and long fluorescence lifetime in water. These properties make it superior to existing genetically encodable fluorescent amino acids for monitoring protein interactions and conformational changes through fluorescence polarization or lifetime experiments, including fluorescence lifetime imaging microscopy (FLIM). Here, we report the genetic incorporation of Acd using engineered pyrrolysine tRNA synthetase (RS) mutants that allow for efficient Acd incorporation in both E. coli and mammalian cells. We compare protein yields and amino acid specificity for these Acd RSs to identify an optimal construct. We also demonstrate the use of Acd in FLIM, where its long lifetime provides strong contrast compared to endogenous fluorophores and engineered fluorescent proteins, which have lifetimes less than 5 ns.
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Affiliation(s)
- Chloe M Jones
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104 USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania 3700 Hamilton Walk Philadelphia PA 19104 USA
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104 USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania 3700 Hamilton Walk Philadelphia PA 19104 USA
| | - Robert J Blizzard
- Department of Biochemistry and Biophysics, Oregon State University 2011 Ag Life Sciences Building Corvallis Oregon 97331 USA
| | - Mika Munari
- Department of Physiology and Biophysics, University of Washington 1705 NE Pacific St., Box 357290 Seattle WA 98195 USA
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104 USA
| | - Tiberiu S Mihaila
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104 USA
| | - Alex J Eddins
- Department of Biochemistry and Biophysics, Oregon State University 2011 Ag Life Sciences Building Corvallis Oregon 97331 USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University 2011 Ag Life Sciences Building Corvallis Oregon 97331 USA
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington 1705 NE Pacific St., Box 357290 Seattle WA 98195 USA
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington 1705 NE Pacific St., Box 357290 Seattle WA 98195 USA
| | - E James Petersson
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania 3700 Hamilton Walk Philadelphia PA 19104 USA
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34
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Lee S, Kim J, Koh M. Recent Advances in Fluorescence Imaging by Genetically Encoded Non-canonical Amino Acids. J Mol Biol 2021; 434:167248. [PMID: 34547330 DOI: 10.1016/j.jmb.2021.167248] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/09/2023]
Abstract
Technical innovations in protein labeling with a fluorophore at the specific residue have played a significant role in studying protein dynamics. The genetic code expansion (GCE) strategy enabled the precise installation of fluorophores at the tailored site of proteins in live cells with minimal perturbation of native functions. Considerable advances have been achieved over the past decades in fluorescent imaging using GCE strategies along with bioorthogonal chemistries. In this review, we discuss advances in the GCE-based strategies to site-specifically introduce fluorophore at a defined position of the protein and their bio-imaging applications.
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Affiliation(s)
- Sanghee Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Minseob Koh
- Department of Chemistry, Pusan National University, Busan 46241, Republic of Korea.
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35
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Bajaj K, Pidiyara K, Khan S, Jha PN, Sakhuja R, Kumar D. Fluorescent glutamine and asparagine as promising probes for chemical biology. Org Biomol Chem 2021; 19:7695-7700. [PMID: 34524312 DOI: 10.1039/d1ob01029h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent probes have become valuable tools in chemical biology, providing interesting inferences for unfolding the complexities of natural biochemical processes. In this study, we report the synthesis and characterization of fluorescent labelled glutamine (Gln) and asparagine (Asn) derivatives via traceless Staudinger ligation, which exhibited high fluorescence quantum yields, excellent photostabilities and emission of blue fluorescence in the visible region. The successful permeation of these fluorescent amino acids into cellular components proved their potential as fluorescent probes for chemical biology.
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Karishma Pidiyara
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Shahid Khan
- Department of Biology, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Prabhat N Jha
- Department of Biology, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Rajeev Sakhuja
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Dalip Kumar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
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36
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Louet M, Casiraghi M, Damian M, Costa MGS, Renault P, Gomes AAS, Batista PR, M'Kadmi C, Mary S, Cantel S, Denoyelle S, Ben Haj Salah K, Perahia D, Bisch PM, Fehrentz JA, Catoire LJ, Floquet N, Banères JL. Concerted conformational dynamics and water movements in the ghrelin G protein-coupled receptor. eLife 2021; 10:e63201. [PMID: 34477105 PMCID: PMC8416020 DOI: 10.7554/elife.63201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
There is increasing support for water molecules playing a role in signal propagation through G protein-coupled receptors (GPCRs). However, exploration of the hydration features of GPCRs is still in its infancy. Here, we combined site-specific labeling with unnatural amino acids to molecular dynamics to delineate how local hydration of the ghrelin receptor growth hormone secretagogue receptor (GHSR) is rearranged upon activation. We found that GHSR is characterized by a specific hydration pattern that is selectively remodeled by pharmacologically distinct ligands and by the lipid environment. This process is directly related to the concerted movements of the transmembrane domains of the receptor. These results demonstrate that the conformational dynamics of GHSR are tightly coupled to the movements of internal water molecules, further enhancing our understanding of the molecular bases of GPCR-mediated signaling.
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Affiliation(s)
- Maxime Louet
- IBMM, Univ Montpellier, CNRS, ENSCMMontpellierFrance
| | - Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550)ParisFrance
| | | | - Mauricio GS Costa
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-SaclayGif-sur-YvetteFrance
- Programa de Computação Científica, Fundação Oswaldo CruzRio de JaneiroBrazil
| | - Pedro Renault
- IBMM, Univ Montpellier, CNRS, ENSCMMontpellierFrance
| | - Antoniel AS Gomes
- IBMM, Univ Montpellier, CNRS, ENSCMMontpellierFrance
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Paulo R Batista
- Programa de Computação Científica, Fundação Oswaldo CruzRio de JaneiroBrazil
| | | | - Sophie Mary
- IBMM, Univ Montpellier, CNRS, ENSCMMontpellierFrance
| | - Sonia Cantel
- IBMM, Univ Montpellier, CNRS, ENSCMMontpellierFrance
| | | | | | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-SaclayGif-sur-YvetteFrance
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | | | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550)ParisFrance
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37
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Gleason PR, Kolbaba-Kartchner B, Henderson JN, Stahl EP, Simmons CR, Mills JH. Structural Origins of Altered Spectroscopic Properties upon Ligand Binding in Proteins Containing a Fluorescent Noncanonical Amino Acid. Biochemistry 2021; 60:2577-2585. [PMID: 34415744 DOI: 10.1021/acs.biochem.1c00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent noncanonical amino acids (fNCAAs) could serve as starting points for the rational design of protein-based fluorescent sensors of biological activity. However, efforts toward this goal are likely hampered by a lack of atomic-level characterization of fNCAAs within proteins. Here, we describe the spectroscopic and structural characterization of five streptavidin mutants that contain the fNCAA l-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) at sites proximal to the binding site of its substrate, biotin. Many of the mutants exhibited altered fluorescence spectra in response to biotin binding, which included both increases and decreases in fluorescence intensity as well as red- or blue-shifted emission maxima. Structural data were also obtained for three of the five mutants. The crystal structures shed light on interactions between 7-HCAA and functional groups, contributed either by the protein or by the substrate, that may be responsible for the observed changes in the 7-HCAA spectra. These data could be used in future studies aimed at the rational design of fluorescent, protein-based sensors of small molecule binding or dissociation.
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38
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Noden M, Taylor SD. Enantioselective Synthesis and Application of Small and Environmentally Sensitive Fluorescent Amino Acids for Probing Biological Interactions. J Org Chem 2021; 86:11407-11418. [PMID: 34387500 DOI: 10.1021/acs.joc.1c00907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Environmentally sensitive fluorescent amino acids (FlAAs) have been used extensively to probe biological interactions. However, most of these amino acids are large and do not resemble amino acid side chains. Here, we report the enantioselective synthesis of two small and environmentally sensitive fluorescent amino acids bearing 7-dialkylaminocoumarin side chains by alkylation of a Ni(II) glycine Schiff base complex. These amino acids exhibit a large increase in fluorescence as environment polarity decreases. One of these FLAAs was incorporated into a highly active analog of the cyclic lipopeptide antibiotic paenibacterin by Fmoc solid-phase peptide synthesis via a new and very efficient route. This peptide was used to probe the interaction of the antibiotic with model liposomes, lipopolysaccharides, and live bacteria.
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Affiliation(s)
- Michael Noden
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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39
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Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods Enzymol 2021; 656:545-571. [PMID: 34325798 DOI: 10.1016/bs.mie.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Proline residues are unique in the extent to which they constrain the conformational space available to the protein backbone. Because the conformational preferences of proline cannot be recapitulated by any of the other proteinogenic amino acids, standard mutagenesis approaches that seek to introduce new chemical functionality at proline positions unavoidably perturb backbone flexibility. Here, we detail the incorporation of proline analogs into recombinant proteins in Escherichia coli via a residue-specific mutagenesis strategy. This approach results in global replacement of proline residues with high yields of the recombinant protein of interest, minimal genetic manipulation, and maintenance of backbone conformational constraints.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States.
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40
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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41
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Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
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42
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Liu Y, Davis RG, Thomas PM, Kelleher NL, Jewett MC. In vitro-Constructed Ribosomes Enable Multi-site Incorporation of Noncanonical Amino Acids into Proteins. Biochemistry 2021; 60:161-169. [PMID: 33426883 DOI: 10.1021/acs.biochem.0c00829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, assembly, and translation (iSAT) system was established to construct functional ribosomes in cell-free systems. However, the iSAT system has not been shown to be compatible with genetic code expansion. Here, to address this gap, we develop an iSAT platform capable of manufacturing pure proteins with site-specifically incorporated ncAAs. We first establish an iSAT platform based on extracts from genomically recoded Escherichia coli lacking release factor 1 (RF-1). This permits complete reassignment of the amber codon translation function. Next, we optimize orthogonal translation system components to demonstrate the benefits of genomic RF-1 deletion on incorporation of ncAAs into proteins. Using our optimized platform, we demonstrate high-level, multi-site incorporation of p-acetyl-phenylalanine (pAcF) and p-azido-phenylalanine into superfolder green fluorescent protein (sfGFP). Mass spectrometry analysis confirms the high accuracy of incorporation for pAcF at one, two, and five amber sites in sfGFP. The iSAT system updated for ncAA incorporation sets the stage for investigating ribosomal mutations to better understand the fundamental basis of protein synthesis, manufacturing proteins with new properties, and engineering ribosomes for novel polymerization chemistries.
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43
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Lee J, Schwarz KJ, Yu H, Krüger A, Anslyn EV, Ellington AD, Moore JS, Jewett MC. Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro. Chem Commun (Camb) 2021; 57:2661-2664. [DOI: 10.1039/d0cc07740b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We expand the substrate scope of ribosome-mediated incorporation to α-amino acids with a variety of fluorescent groups on the sidechain.
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Affiliation(s)
- Joongoo Lee
- Department of Chemical and Biological Engineering and Center for Synthetic Biology
- Northwestern University
- Evanston
- USA
| | - Kevin J. Schwarz
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Hao Yu
- Departments of Chemical and Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering and Center for Synthetic Biology
- Northwestern University
- Evanston
- USA
| | - Eric V. Anslyn
- Department of Chemistry and Biochemistry
- University of Texas at Austin
- Austin
- USA
| | - Andrew D. Ellington
- Department of Chemistry and Biochemistry
- Institute for Cellular and Molecular Biology
- University of Texas at Austin
- Austin
- USA
| | - Jeffrey S. Moore
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- Urbana
- USA
- Beckman Institute for Advanced Science and Technology
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology
- Northwestern University
- Evanston
- USA
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44
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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45
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Tang J, Yu C, Loredo A, Chen Y, Xiao H. Site-Specific Incorporation of a Photoactivatable Fluorescent Amino Acid. Chembiochem 2020; 22:501-504. [PMID: 32961013 DOI: 10.1002/cbic.202000602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/21/2020] [Indexed: 12/11/2022]
Abstract
Photoactivatable fluorophores are emerging optical probes for biological applications. Most photoactivatable fluorophores are relatively large in size and need to be activated by ultraviolet light; this dramatically limits their applications. To introduce photoactivatable fluorophores into proteins, recent investigations have explored several protein-labeling technologies, including fluorescein arsenical hairpin (FlAsH) Tag, HaloTag labeling, SNAPTag labeling, and other bioorthogonal chemistry-based methods. However, these technologies require a multistep labeling process. Here, by using genetic code expansion and a single sulfur-for-oxygen atom replacement within an existing fluorescent amino acid, we have site-specifically incorporated the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) into proteins in a single step. Moreover, upon exposure to visible light, SAcd can be efficiently desulfurized to its oxo derivatives, thus restoring the strong fluorescence of labeled proteins.
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Affiliation(s)
- Juan Tang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Chenfei Yu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Axel Loredo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Yuda Chen
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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46
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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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47
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A rationally designed orthogonal synthetase for genetically encoded fluorescent amino acids. Heliyon 2020; 6:e05140. [PMID: 33083608 PMCID: PMC7550906 DOI: 10.1016/j.heliyon.2020.e05140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 01/25/2023] Open
Abstract
The incorporation of non-canonical amino acids into proteins has emerged as a promising strategy to manipulate and study protein structure-function relationships with superior precision in vitro and in vivo. To date, fluorescent non-canonical amino acids (f-ncAA) have been successfully incorporated in proteins expressed in bacterial systems, Xenopus oocytes, and HEK-293T cells. Here, we describe the rational generation of a novel orthogonal aminoacyl-tRNA synthetase based on the E. coli tyrosine synthetase that is capable of encoding the f-ncAA tyr-coumarin in HEK-293T cells.
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48
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Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
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Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
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49
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Wu Y, Tam WS, Chau HF, Kaur S, Thor W, Aik WS, Chan WL, Zweckstetter M, Wong KL. Solid-phase fluorescent BODIPY-peptide synthesis via in situ dipyrrin construction. Chem Sci 2020; 11:11266-11273. [PMID: 34094367 PMCID: PMC8162834 DOI: 10.1039/d0sc04849f] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 12/28/2022] Open
Abstract
Traditional fluorescent peptide chemical syntheses hinge on the use of limited fluorescent/dye-taggable unnatural amino acids and entail multiple costly purifications. Here we describe a facile and efficient protocol for in situ construction of dipyrrins on the N-terminus with 20 natural and five unnatural amino acids and the lysine's side chain of selected peptides/peptide drugs through Fmoc-based solid-phase peptide synthesis. The new strategy enables the direct formation of boron-dipyrromethene (BODIPY)-peptide conjugates from simple aldehyde and pyrrole derivatives without pre-functionalization, and only requires a single-time chromatographic purification at the final stage. As a model study, synthesized EBNA1-targeting BODIPY1-Pep4 demonstrates intact selectivity in vitro, responsive fluorescence enhancement, and higher light cytotoxicity due to the photo-generation of cytotoxic singlet oxygen. This work offers a novel practical synthetic platform for fluorescent peptides for multifaceted biomedical applications.
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Affiliation(s)
- Yue Wu
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Wing-Sze Tam
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Ho-Fai Chau
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Simranjeet Kaur
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Waygen Thor
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Wei Shen Aik
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Wai-Lun Chan
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- German Center for Neurodegenerative Diseases (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Germany
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- German Center for Neurodegenerative Diseases (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Germany
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
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50
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Henderson JN, Simmons CR, Fahmi NE, Jeffs JW, Borges CR, Mills JH. Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore. Biochemistry 2020; 59:3401-3410. [PMID: 32845612 DOI: 10.1021/acs.biochem.0c00474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetically encoded fluorescent noncanonical amino acids (fNCAAs) could be used to develop novel fluorescent sensors of protein function. Previous efforts toward this goal have been limited by the lack of extensive physicochemical and structural characterizations of protein-based sensors containing fNCAAs. Here, we report the steady-state spectroscopic properties and first structural analyses of an fNCAA-containing Fab fragment of the 5c8 antibody, which binds human CD40L. A previously reported 5c8 variant in which the light chain residue IleL98 is replaced with the fNCAA l-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) exhibits a 1.7-fold increase in fluorescence upon antigen binding. Determination and comparison of the apparent pKas of 7-HCAA in the unbound and bound forms indicate that the observed increase in fluorescence is not the result of perturbations in pKa. Crystal structures of the fNCAA-containing Fab in the apo and bound forms reveal interactions between the 7-HCAA side chain and surrounding residues that are disrupted upon antigen binding. This structural characterization not only provides insight into the manner in which protein environments can modulate the fluorescence properties of 7-HCAA but also could serve as a starting point for the rational design of new fluorescent protein-based reporters of protein function.
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Affiliation(s)
- J Nathan Henderson
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Chad R Simmons
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Nour Eddine Fahmi
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Joshua W Jeffs
- The Biodesign Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, Arizona 85287, United States.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chad R Borges
- The Biodesign Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, Arizona 85287, United States.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Jeremy H Mills
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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