1
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Niu W, Guo J. Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology. Chem Rev 2024. [PMID: 39207844 DOI: 10.1021/acs.chemrev.3c00938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Over the past two decades, genetic code expansion (GCE)-enabled methods for incorporating noncanonical amino acids (ncAAs) into proteins have significantly advanced the field of synthetic biology while also reaping substantial benefits from it. On one hand, they provide synthetic biologists with a powerful toolkit to enhance and diversify biological designs beyond natural constraints. Conversely, synthetic biology has not only propelled the development of ncAA incorporation through sophisticated tools and innovative strategies but also broadened its potential applications across various fields. This Review delves into the methodological advancements and primary applications of site-specific cellular incorporation of ncAAs in synthetic biology. The topics encompass expanding the genetic code through noncanonical codon addition, creating semiautonomous and autonomous organisms, designing regulatory elements, and manipulating and extending peptide natural product biosynthetic pathways. The Review concludes by examining the ongoing challenges and future prospects of GCE-enabled ncAA incorporation in synthetic biology and highlighting opportunities for further advancements in this rapidly evolving field.
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Affiliation(s)
- Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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2
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Guo Y, Cheng L, Hu Y, Zhang M, Liu R, Wang Y, Jiang S, Xiao H. Biosynthesis of Halogenated Tryptophans for Protein Engineering Using Genetic Code Expansion. Chembiochem 2024:e202400366. [PMID: 38958600 DOI: 10.1002/cbic.202400366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/04/2024]
Abstract
Genetic Code Expansion technology offers significant potential in incorporating noncanonical amino acids into proteins at precise locations, allowing for the modulation of protein structures and functions. However, this technology is often limited by the need for costly and challenging-to-synthesize external noncanonical amino acid sources. In this study, we address this limitation by developing autonomous cells capable of biosynthesizing halogenated tryptophan derivatives and introducing them into proteins using Genetic Code Expansion technology. By utilizing inexpensive halide salts and different halogenases, we successfully achieve the selective biosynthesis of 6-chloro-tryptophan, 7-chloro-tryptophan, 6-bromo-tryptophan, and 7-bromo-tryptophan. These derivatives are introduced at specific positions with corresponding bioorthogonal aminoacyl-tRNA synthetase/tRNA pairs in response to the amber codon. Following optimization, we demonstrate the robust expression of proteins containing halogenated tryptophan residues in cells with the ability to biosynthesize these tryptophan derivatives. This study establishes a versatile platform for engineering proteins with various halogenated tryptophans.
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Affiliation(s)
- Yiming Guo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Linqi Cheng
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Yu Hu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Mengxi Zhang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Rui Liu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Yixian Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Shiyu Jiang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
- SynthX Center, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas, 77005, USA
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3
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Chen W, Sullivan MO. Unnatural Amino Acid Engineering for Intracellular Delivery of Protein Therapeutics. Methods Mol Biol 2024; 2720:151-164. [PMID: 37775664 DOI: 10.1007/978-1-0716-3469-1_11] [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] [Indexed: 10/01/2023]
Abstract
Protein drugs are a critically important therapeutic modality due to the sophisticated binding recognition, catalytic properties, and disease relevance of proteins. There is a clear need for new strategies able to improve pharmacokinetics, bioavailability, and/or intracellular delivery of therapeutic proteins, as stability limitations have significantly hindered clinical advancement, and most proteins are membrane impermeable. Bioconjugation strategies able to site-specifically modify proteins with cell binding, and other ligands offer a particularly valuable approach to facilitate protein delivery due to the importance of ligand presentation on protein bioactivity and cellular uptake. We explored unnatural amino acid (UAA) incorporation as a novel strategy to tunably incorporate clustered cell-binding ligands in fluorescent proteins and suicide enzymes, resulting in substantial increases in cell-specific uptake and targeted cell-killing activity. These approaches offer a valuable and versatile method to modify a variety of proteins and enable improved clinical potential.
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Affiliation(s)
- Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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4
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Esteves CIC, Raposo MMM, Costa SPG. New Amino Acid-Based Thiosemicarbazones and Hydrazones: Synthesis and Evaluation as Fluorimetric Chemosensors in Aqueous Mixtures. Molecules 2023; 28:7256. [PMID: 37959675 PMCID: PMC10650509 DOI: 10.3390/molecules28217256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/25/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Bearing in mind the interest in the development and application of amino acids/peptides as bioinspired systems for sensing, a series of new phenylalanine derivatives bearing thiosemicarbazone and hydrazone units at the side chain were synthesised and evaluated as fluorimetric chemosensors for ions. Thiosemicarbazone and hydrazone moieties were chosen because they are considered both proton-donor and proton-acceptor, which is an interesting feature in the design of chemosensors. The obtained compounds were tested for the recognition of organic and inorganic anions (such as AcO-, F-, Cl-, Br-, I-, ClO4-, CN-, NO3-, BzO-, OH-, H2PO4- and HSO4-) and of alkaline, alkaline-earth, and transition metal cations, (such as Na+, K+, Cs+, Ag+, Cu+, Cu2+, Ca2+, Cd2+, Co2+, Pb2+, Pd2+, Ni2+, Hg2+, Zn2+, Fe2+, Fe3+ and Cr3+) in acetonitrile and its aqueous mixtures in varying ratios via spectrofluorimetric titrations. The results indicate that there is a strong interaction via the donor N, O and S atoms at the side chain of the various phenylalanines, with higher sensitivity for Cu2+, Fe3+ and F- in a 1:2 ligand-ion stoichiometry. The photophysical and metal ion-sensing properties of these phenylalanines suggest that they might be suitable for incorporation into peptide chemosensory frameworks.
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Affiliation(s)
| | | | - Susana P. G. Costa
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (C.I.C.E.); (M.M.M.R.)
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5
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Krueger TD, Chen C, Fang C. Targeting Ultrafast Spectroscopic Insights into Red Fluorescent Proteins. Chem Asian J 2023; 18:e202300668. [PMID: 37682793 DOI: 10.1002/asia.202300668] [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: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/10/2023]
Abstract
Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs across the imaging and life sciences. Since the rational design of RFPs with improved functions or enhanced versatility requires a mechanistic understanding of their working mechanisms, while fluorescence is intrinsically an ultrafast event, a suitable toolset involving steady-state and time-resolved spectroscopic techniques has become powerful in delineating key structural features and dynamic steps which govern irreversible photoconverting or reversible photoswitching RFPs, and large Stokes shift (LSS)RFPs. The pertinent cis-trans isomerization and protonation state change of RFP chromophores in their local environments, involving key residues in protein matrices, lead to rich and complicated spectral features across multiple timescales. In particular, ultrafast excited-state proton transfer in various LSSRFPs showcases the resolving power of wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in mapping a photocycle with crucial knowledge about the red-emitting species. Moreover, recent progress in noncanonical RFPs with a site-specifically modified chromophore provides an appealing route for efficient engineering of redder and brighter RFPs, highly desirable for bioimaging. Such an effective feedback loop involving physical chemists, protein engineers, and biomedical microscopists will enable future successes to expand fundamental knowledge and improve human health.
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Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
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6
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Zhang J, Li Z, Pang Y, Fan Y, Ai HW. Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor. ACS Sens 2023; 8:2996-3003. [PMID: 37480329 PMCID: PMC10663054 DOI: 10.1021/acssensors.3c00409] [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] [Indexed: 07/24/2023]
Abstract
There is great interest in developing boronolectins that are synthetic lectin mimics containing a boronic acid functional group for reversible recognition of diol-containing molecules, such as glycans and ribonucleotides. However, it remains a significant challenge to gain specificity. Here, we present a genetically encoded boronolectin which is a hybrid protein consisting of a noncanonical amino acid (ncAA) p-boronophenylalanine (pBoF), natural-lectin-derived peptide sequences, and a circularly permuted red fluorescent protein (cpRFP). The genetic encodability permitted a straightforward protein engineering process to derive a red fluorescent biosensor that can specifically bind uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), an important nucleotide sugar involved in metabolic sensing and cell signaling. We further characterized the resultant boronic acid- and peptide-assisted UDP-GlcNAc sensor (bapaUGAc) both in vitro and in live mammalian cells. Because UDP-GlcNAc in the endoplasmic reticulum (ER) and Golgi apparatus plays essential roles in glycosylating biomolecules in the secretory pathway, we genetically expressed bapaUGAc in the ER and Golgi and validated the sensor for its responses to metabolic disruption and pharmacological inhibition. In addition, we combined bapaUGAc with UGAcS, a recently reported green fluorescent UDP-GlcNAc sensor based on an alternative sensing mechanism, to monitor UDP-GlcNAc level changes in the ER and cytosol simultaneously. We expect our work to facilitate the future development of specific boronolectins for carbohydrates. In addition, this newly developed genetically encoded bapaUGAc sensor will be a valuable tool for studying UDP-GlcNAc and glycobiology.
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Affiliation(s)
- Jing Zhang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Zefan Li
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Yu Pang
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904, USA
| | - Yichong Fan
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, 22903, USA
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7
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Pang Y, Huang M, Fan Y, Yeh HW, Xiong Y, Ng HL, Ai HW. Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor. ACS Chem Biol 2023; 18:1388-1397. [PMID: 37185019 PMCID: PMC10330634 DOI: 10.1021/acschembio.3c00139] [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] [Indexed: 05/17/2023]
Abstract
Boronic acid-containing fluorescent molecules have been widely used to sense hydrogen peroxide and peroxynitrite, which are important reactive oxygen and nitrogen species in biological systems. However, it has been challenging to gain specificity. Our previous studies developed genetically encoded, green fluorescent peroxynitrite biosensors by genetically incorporating a boronic acid-containing noncanonical amino acid (ncAA), p-boronophenylalanine (pBoF), into the chromophore of circularly permuted green fluorescent proteins (cpGFPs). In this work, we introduced pBoF to amino acid residues spatially close to the chromophore of an enhanced circularly permuted red fluorescent protein (ecpApple). Our effort has resulted in two responsive ecpApple mutants: one bestows reactivity toward both peroxynitrite and hydrogen peroxide, while the other, namely, pnRFP, is a selective red fluorescent peroxynitrite biosensor. We characterized pnRFP in vitro and in live mammalian cells. We further studied the structure and sensing mechanism of pnRFP using X-ray crystallography, 11B-NMR, and computational methods. The boron atom in pnRFP adopts an sp2-hybridization geometry in a hydrophobic pocket, and the reaction of pnRFP with peroxynitrite generates a product with a twisted chromophore, corroborating the observed "turn-off" fluorescence response. Thus, this study extends the color palette of genetically encoded peroxynitrite biosensors, provides insight into the response mechanism of the new biosensor, and demonstrates the versatility of using protein scaffolds to modulate chemoreactivity.
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Affiliation(s)
- Yu Pang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mian Huang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Yichong Fan
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Hsien-Wei Yeh
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Ying Xiong
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ho Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- The UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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8
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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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9
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Batista PMR, Martins CDF, Raposo MMM, Costa SPG. Novel Crown Ether Amino Acids as Fluorescent Reporters for Metal Ions. Molecules 2023; 28:molecules28083326. [PMID: 37110560 PMCID: PMC10140843 DOI: 10.3390/molecules28083326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Unnatural amino acids with enhanced properties, such as increased complexing ability and luminescence, are considered to be highly attractive building blocks for bioinspired frameworks, such as probes for biomolecule dynamics, sensitive fluorescent chemosensors, and peptides for molecular imaging, among others. Therefore, a novel series of highly emissive heterocyclic alanines bearing a benzo[d]oxazolyl unit functionalized with different heterocyclic π-spacers and (aza)crown ether moieties was synthesized. The new compounds were completely characterized using the usual spectroscopic techniques and evaluated as fluorimetric chemosensors in acetonitrile and aqueous mixtures in the presence of various alkaline, alkaline-earth, and transition metal ions. The different crown ether binding moieties as well as the electronic nature of the π-bridge allowed for fine tuning of the sensory properties of these unnatural amino acids towards Pd2+ and Fe3+, as seen by spectrofluorimetric titrations.
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Affiliation(s)
- Patrícia M R Batista
- Centre of Chemistry, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Cátia D F Martins
- Centre of Chemistry, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - M Manuela M Raposo
- Centre of Chemistry, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Susana P G Costa
- Centre of Chemistry, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
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10
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Hayun H, Coban M, Bhagat AK, Ozer E, Alfonta L, Caulfield TR, Radisky ES, Papo N. Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14. Sci Rep 2023; 13:5186. [PMID: 36997589 PMCID: PMC10063552 DOI: 10.1038/s41598-023-32019-3] [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: 01/05/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn2+-containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn2+ ion (S2, S69, A70, L100) or with a structural Ca2+ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling provided an indication of how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn2+, the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. Our findings illustrate how incorporation of NCAAs can be used to probe-and possibly exploit-differential tolerance for substitution within closely related protein-protein complexes as a means to improve specificity.
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Affiliation(s)
- Hezi Hayun
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel
| | - Matt Coban
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, 310 Griffin Building, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ashok Kumar Bhagat
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Thomas R Caulfield
- Departments of Neuroscience, Artificial Intelligence and Informatics, Computational Biology and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Jacksonville, FL, 32224, USA.
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, 310 Griffin Building, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel.
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11
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Zhang J, Li Z, Pang Y, Fan Y, Ai HW. Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530644. [PMID: 36909602 PMCID: PMC10002721 DOI: 10.1101/2023.03.01.530644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
There is great interest in developing boronolectins, which are synthetic lectin mimics containing a boronic acid functional group for reversible recognition of diol-containing molecules, such as glycans and ribonucleotides. However, it remains a significant challenge to gain specificity. Here, we present a genetically encoded boronolectin, which is a hybrid protein consisting of a noncanonical amino acid (ncAA) p-boronophenylalanine (pBoF), natural-lectin-derived peptide sequences, and a circularly permuted red fluorescent protein (cpRFP). The genetic encodability permitted a straightforward protein engineering process to derive a red fluorescent biosensor that can specifically bind uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), an important nucleotide sugar involved in metabolic sensing and cell signaling. We further characterized the resultant boronic acid-and peptide-assisted UDP-GlcNAc sensor (bapaUGAc) both in vitro and in live mammalian cells. Because UDP-GlcNAc in the endoplasmic reticulum (ER) and Golgi apparatus plays essential roles in glycosylating biomolecules in the secretory pathway, we genetically expressed bapaUGAc in the ER and Golgi and validated the sensor for its responses to metabolic disruption and pharmacological inhibition. In addition, we combined bapaUGAc with UGAcS, a recently reported green fluorescent UDP-GlcNAc sensor based on an alternative sensing mechanism, to monitor UDP-GlcNAc level changes in the ER and cytosol simultaneously. We expect our work to facilitate the future development of specific boronolectins for carbohydrates. In addition, this newly developed genetically encoded bapaUGAc sensor will be a valuable tool for studying UDP-GlcNAc and glycobiology.
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Affiliation(s)
- Jing Zhang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Zefan Li
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Yu Pang
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904, USA
| | - Yichong Fan
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Ave, Charlottesville, Virginia, 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, 22903, USA
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12
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Wu K, Moore JA, Miller MD, Chen Y, Lee C, Xu W, Peng Z, Duan Q, Phillips GN, Uribe RA, Xiao H. Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid. Protein Sci 2022; 31:e4443. [PMID: 36173166 PMCID: PMC9601876 DOI: 10.1002/pro.4443] [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: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 01/31/2023]
Abstract
Genetic code expansion technology allows for the use of noncanonical amino acids (ncAAs) to create semisynthetic organisms for both biochemical and biomedical applications. However, exogenous feeding of chemically synthesized ncAAs at high concentrations is required to compensate for the inefficient cellular uptake and incorporation of these components into proteins, especially in the case of eukaryotic cells and multicellular organisms. To generate organisms capable of autonomously biosynthesizing an ncAA and incorporating it into proteins, we have engineered a metabolic pathway for the synthesis of O-methyltyrosine (OMeY). Specifically, we endowed organisms with a marformycins biosynthetic pathway-derived methyltransferase that efficiently converts tyrosine to OMeY in the presence of the co-factor S-adenosylmethionine. The resulting cells can produce and site-specifically incorporate OMeY into proteins at much higher levels than cells exogenously fed OMeY. To understand the structural basis for the substrate selectivity of the transferase, we solved the X-ray crystal structures of the ligand-free and tyrosine-bound enzymes. Most importantly, we have extended this OMeY biosynthetic system to both mammalian cells and the zebrafish model to enhance the utility of genetic code expansion. The creation of autonomous eukaryotes using a 21st amino acid will make genetic code expansion technology more applicable to multicellular organisms, providing valuable vertebrate models for biological and biomedical research.
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Affiliation(s)
- Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Joshua A. Moore
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Biochemistry and Cell Biology ProgramRice UniversityHoustonTexasUSA
| | | | - Yuda Chen
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Catherine Lee
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Weijun Xu
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | - Zane Peng
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Qinghui Duan
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - George N. Phillips
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | - Rosa A. Uribe
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Biochemistry and Cell Biology ProgramRice UniversityHoustonTexasUSA
| | - Han Xiao
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
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13
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Chen Y, He X, Ma B, Liu K, Gao T, Niu W, Guo J. Noncanonical amino acid mutagenesis in response to recoding signal-enhanced quadruplet codons. Nucleic Acids Res 2022; 50:e94. [PMID: 35657094 PMCID: PMC9458425 DOI: 10.1093/nar/gkac474] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
While amber suppression is the most common approach to introduce noncanonical amino acids into proteins in live cells, quadruplet codon decoding has potential to enable a greatly expanded genetic code with up to 256 new codons for protein biosynthesis. Since triplet codons are the predominant form of genetic code in nature, quadruplet codon decoding often displays limited efficiency. In this work, we exploited a new approach to significantly improve quadruplet UAGN and AGGN (N = A, U, G, C) codon decoding efficiency by using recoding signals imbedded in mRNA. With representative recoding signals, the expression level of mutant proteins containing UAGN and AGGN codons reached 48% and 98% of that of the wild-type protein, respectively. Furthermore, this strategy mitigates a common concern of reading-through endogenous stop codons with amber suppression-based system. Since synthetic recoding signals are rarely found near the endogenous UAGN and AGGN sequences, a low level of undesirable suppression is expected. Our strategy will greatly enhance the utility of noncanonical amino acid mutagenesis in live-cell studies.
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Affiliation(s)
- Yan Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Kun Liu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Tianyu Gao
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 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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14
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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15
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Zeynaloo E, Zahran EM, Yang YP, Dikici E, Head T, Bachas LG, Daunert S. Reagentless electrochemical biosensors through incorporation of unnatural amino acids on the protein structure. Biosens Bioelectron 2022; 200:113861. [PMID: 34986438 PMCID: PMC9404255 DOI: 10.1016/j.bios.2021.113861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/19/2021] [Accepted: 12/01/2021] [Indexed: 11/19/2022]
Abstract
Typical protein biosensors employ chemical or genetic labeling of the protein, thus introducing an extraneous molecule to the wild-type parent protein, often changing the overall structure and properties of the protein. While these labeling methods have proven successful in many cases, they also have a series of disadvantages associated with their preparation and function. An alternative route for labeling proteins is the incorporation of unnatural amino acid (UAA) analogues, capable of acting as a label, into the structure of a protein. Such an approach, while changing the local microenvironment, poses less of a burden on the overall structure of the protein. L-DOPA is an analog of phenylalanine and contains a catechol moiety that participates in a quasi-reversible, two-electron redox process, thus making it suitable as an electrochemical label/reporter. The periplasmic glucose/galactose binding protein (GBP) was chosen to demonstrate this detection principle. Upon glucose binding, GBP undergoes a significant conformational change that is manifested as a change in the electrochemistry of L-DOPA. The electroactive GBP was immobilized onto gold nanoparticle-modified, polymerized caffeic acid, screen-printed carbon electrodes (GBP-LDOPA/AuNP/PCA/SPCE) for the purpose of direct measurement of glucose levels and serves as a proof-of-concept of the use of electrochemically-active unnatural amino acids as the label. The resulting reagentless GBP biosensors exhibited a highly selective and sensitive binding affinity for glucose in the micromolar range, laying the foundation for a new biosensing methodology based on global incorporation of an electroactive amino acid into the protein's primary sequence for highly selective electrochemical detection of compounds of interest.
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Affiliation(s)
- Elnaz Zeynaloo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Department of Chemistry, University of Miami, Miami, FL, 33134, United States
| | - Elsayed M Zahran
- Department of Chemistry, Ball State University, Muncie, IN, 47306, United States
| | - Yu-Ping Yang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States; Clinical and Translational Science Institute, University of Miami, Miami, FL, 33136, United States
| | - Trajen Head
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States
| | - Leonidas G Bachas
- Department of Chemistry, University of Miami, Miami, FL, 33134, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States; Clinical and Translational Science Institute, University of Miami, Miami, FL, 33136, United States.
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16
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Shatsauskas AL, Zablotskii YА, Chernenko SА, Zheleznova TY, Shuvalov VY, Kostyuchenko AS, Fisyuk AS. Synthesis and photophysical properties of the products of the reaction of 5-methyl-7-phenyl[1,3]oxazolo[5,4-b]pyridin-2(1H)-one with amino acids. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-021-03045-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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18
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Erdogan YC, Altun HY, Secilmis M, Ata BN, Sevimli G, Cokluk Z, Zaki AG, Sezen S, Akgul Caglar T, Sevgen İ, Steinhorn B, Ai H, Öztürk G, Belousov VV, Michel T, Eroglu E. Complexities of the chemogenetic toolkit: Differential mDAAO activation by d-amino substrates and subcellular targeting. Free Radic Biol Med 2021; 177:132-142. [PMID: 34687864 PMCID: PMC8639799 DOI: 10.1016/j.freeradbiomed.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023]
Abstract
A common approach to investigate oxidant-regulated intracellular pathways is to add exogenous H2O2 to living cells or tissues. However, the addition of H2O2 to the culture medium of cells or tissues approach does not accurately replicate intracellular redox-mediated cell responses. d-amino acid oxidase (DAAO)-based chemogenetic tools represent informative methodological advances that permit the generation of H2O2 on demand with a high spatiotemporal resolution by providing or withdrawing the DAAO substrate d-amino acids. Much has been learned about the intracellular transport of H2O2 through studies using DAAO, yet these valuable tools remain incompletely characterized in many cultured cells. In this study, we describe and characterize in detail the features of a new modified variant of DAAO (termed mDAAO) with improved catalytic activities. We tested mDAAO functionality in several cultured cell lines employing live-cell imaging techniques. Our imaging experiments show that mDAAO is suitable for the generation of H2O2 under hypoxic conditions imaged with the novel ultrasensitive H2O2 sensor (HyPer7). Moreover, this approach was suitable for generating H2O2 in a reversible and concentration-dependent manner in subcellular locales. Furthermore, we show that the choice of d-amino acids differentially affects mDAAO-dependent intracellular H2O2 generation. When paired with the hydrogen sulfide (H2S) sensor hsGFP, administration of the sulfur-containing amino acid d-cysteine to cells expressing mDAAO generates robust H2S signals. We also show that chemogenetic H2O2 generation in different cell types yields distinct HyPer7 profiles. These studies fully characterize the new mDAAO as a novel chemogenetic tool and provide multiparametric approaches for cell manipulation that may open new lines of investigations for redox biochemists to dissect the role of ROS signaling pathways with high spatial and temporal precision.
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Affiliation(s)
- Yusuf C Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hamza Y Altun
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Busra N Ata
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Serap Sezen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Tuba Akgul Caglar
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - İlker Sevgen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Benjamin Steinhorn
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Huiwang Ai
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Physiology Department, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Vsevelod V Belousov
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Institute of Cardiovascular Physiology, Universitätsmedizin Göttingen, 37073, Göttingen, Germany
| | - Thomas Michel
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey; Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Austria; Nanotechnology Research and Application Center, Sabanci University, Istanbul, Turkey.
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19
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Aarthy M, George A, Ayyadurai N. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review. Int J Biol Macromol 2021; 191:840-851. [PMID: 34560154 DOI: 10.1016/j.ijbiomac.2021.09.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.
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Affiliation(s)
- Mayilvahanan Aarthy
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Augustine George
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Niraikulam Ayyadurai
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India.
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20
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King EA, Peairs EM, Uthappa DM, Villa JK, Goff CM, Burrow NK, Deitch RT, Martin AK, Young DD. Photoregulation of PRMT-1 Using a Photolabile Non-Canonical Amino Acid. Molecules 2021; 26:molecules26165072. [PMID: 34443661 PMCID: PMC8398576 DOI: 10.3390/molecules26165072] [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: 07/15/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022] Open
Abstract
Protein methyltransferases are vital to the epigenetic modification of gene expression. Thus, obtaining a better understanding of and control over the regulation of these crucial proteins has significant implications for the study and treatment of numerous diseases. One ideal mechanism of protein regulation is the specific installation of a photolabile-protecting group through the use of photocaged non-canonical amino acids. Consequently, PRMT1 was caged at a key tyrosine residue with a nitrobenzyl-protected Schultz amino acid to modulate protein function. Subsequent irradiation with UV light removes the caging group and restores normal methyltransferase activity, facilitating the spatial and temporal control of PRMT1 activity. Ultimately, this caged PRMT1 affords the ability to better understand the protein’s mechanism of action and potentially regulate the epigenetic impacts of this vital protein.
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21
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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: 53] [Impact Index Per Article: 17.7] [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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22
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Auhim HS, Grigorenko BL, Harris TK, Aksakal OE, Polyakov IV, Berry C, Gomes GDP, Alabugin IV, Rizkallah PJ, Nemukhin AV, Jones DD. Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step. Chem Sci 2021; 12:7735-7745. [PMID: 34168826 PMCID: PMC8188506 DOI: 10.1039/d0sc06693a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/26/2021] [Indexed: 11/24/2022] Open
Abstract
Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an "open" conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.
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Affiliation(s)
- Husam Sabah Auhim
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
- Department of Biology, College of Science, University of Baghdad Baghdad Iraq
| | - Bella L Grigorenko
- Chemistry Department, Lomonosov Moscow State University Leninskie Gory, 1-3 Moscow Russian Federation +7 495 939 1096
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences Moscow Russian Federation
| | - Tessa K Harris
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
| | - Ozan E Aksakal
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
| | - Igor V Polyakov
- Chemistry Department, Lomonosov Moscow State University Leninskie Gory, 1-3 Moscow Russian Federation +7 495 939 1096
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences Moscow Russian Federation
| | - Colin Berry
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
| | - Gabriel Dos Passos Gomes
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada
- Department of Computer Science, University of Toronto 214 College St. Toronto Ontario M5T 3A1 Canada
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University Tallahassee Fl 32306 USA +1 850 644 5795
| | | | - Alexander V Nemukhin
- Chemistry Department, Lomonosov Moscow State University Leninskie Gory, 1-3 Moscow Russian Federation +7 495 939 1096
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences Moscow Russian Federation
| | - D Dafydd Jones
- School of Biosciences, Molecular Biosciences Division, Cardiff University Sir Martin Evans Building Cardiff CF10 3AX UK +44 (0)29 2087 4290
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23
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Yuan Z, Liu X, Liu C, Zhang Y, Rao Y. Recent Advances in Rapid Synthesis of Non-proteinogenic Amino Acids from Proteinogenic Amino Acids Derivatives via Direct Photo-Mediated C-H Functionalization. Molecules 2020; 25:E5270. [PMID: 33198166 PMCID: PMC7696505 DOI: 10.3390/molecules25225270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
Non-proteinogenic amino acids have attracted tremendous interest for their essential applications in the realm of biology and chemistry. Recently, rising C-H functionalization has been considered an alternative powerful method for the direct synthesis of non-proteinogenic amino acids. Meanwhile, photochemistry has become popular for its predominant advantages of mild conditions and conservation of energy. Therefore, C-H functionalization and photochemistry have been merged to synthesize diverse non-proteinogenic amino acids in a mild and environmentally friendly way. In this review, the recent developments in the photo-mediated C-H functionalization of proteinogenic amino acids derivatives for the rapid synthesis of versatile non-proteinogenic amino acids are presented. Moreover, postulated mechanisms are also described wherever needed.
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Affiliation(s)
- Zhenbo Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
| | - Xuanzhong Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
| | - Changmei Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
| | - Yan Zhang
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China;
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
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24
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Lieser RM, Yur D, Sullivan MO, Chen W. Site-Specific Bioconjugation Approaches for Enhanced Delivery of Protein Therapeutics and Protein Drug Carriers. Bioconjug Chem 2020; 31:2272-2282. [DOI: 10.1021/acs.bioconjchem.0c00456] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rachel M. Lieser
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Daniel Yur
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Millicent O. Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
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25
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Chen Y, Tang J, Wang L, Tian Z, Cardenas A, Fang X, Chatterjee A, Xiao H. Creation of Bacterial cells with 5-Hydroxytryptophan as a 21 st Amino Acid Building Block. Chem 2020; 6:2717-2727. [PMID: 33102928 DOI: 10.1016/j.chempr.2020.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While most organisms utilize 20 canonical amino acid building blocks for protein synthesis, adding additional candidates to the amino acid repertoire can greatly facilitate the investigation and manipulation of protein structures and functions. In this study, we report the generation of completely autonomous organisms with a 21st ncAA, 5-hydroxytryptophan (5HTP). Like 20 canonical amino acids, 5-hydroxytryptophan can be biosynthesized in vivo from simple carbon sources and is subsequently incorporated into proteins in response to the amber stop codon. Using this unnatural organism, we have prepared a single-chain immunoglobulin variable fragment conjugated with a fluorophore and demonstrated the utility of these autonomous cells to monitor oxidative stress. Creation of this and other cells containing the 21st amino acid will provide an opportunity to generate proteins and organisms with novel activities, as well as to determine the evolutionary consequences of using additional amino acid buildings.
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Affiliation(s)
- Yuda Chen
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Juan Tang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Lushun Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Zeru Tian
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Adam Cardenas
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Xinlei Fang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, U.S.A
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A.,Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A.,Lead Contact
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26
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Zhang Y, Du Y, Li M, Zhang D, Xiang Z, Peng T. Activity‐Based Genetically Encoded Fluorescent and Luminescent Probes for Detecting Formaldehyde in Living Cells. Angew Chem Int Ed Engl 2020; 59:16352-16356. [DOI: 10.1002/anie.202001425] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/06/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Yuqing Zhang
- State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Yimeng Du
- State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Manjia Li
- State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Dong Zhang
- State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China
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27
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Zhang Y, Du Y, Li M, Zhang D, Xiang Z, Peng T. Activity‐Based Genetically Encoded Fluorescent and Luminescent Probes for Detecting Formaldehyde in Living Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuqing Zhang
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate School Shenzhen 518055 China
| | - Yimeng Du
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate School Shenzhen 518055 China
| | - Manjia Li
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate School Shenzhen 518055 China
| | - Dong Zhang
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate School Shenzhen 518055 China
| | - Zheng Xiang
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate School Shenzhen 518055 China
| | - Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate School Shenzhen 518055 China
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28
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Design of fluorescent protein-based sensors through a general protection-deprotection strategy. Methods Enzymol 2020; 640:63-82. [PMID: 32560806 DOI: 10.1016/bs.mie.2020.04.003] [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: 02/25/2023]
Abstract
Engineered fluorescent proteins have been extensively used in biological research for the study of gene expression, protein function and trafficking, and protein-protein interactions. In addition, fluorescent proteins have also been engineered to act as biosensing agents to detect intracellular signaling molecules and other small-molecule metabolites. Although they have been engineered extensively to achieve novel properties, fluorescent proteins are traditionally modified using the 20 canonical amino acids. This limits the number of functional groups that are available to the design and construction of novel fluorescent proteins. The expansion of the genetic code through the incorporation of noncanonical amino acids presents an opportunity to add new functionalities with the intent of modifying chemical and physical properties of fluorescent proteins. Herein we provide a general procedure for the site-specific incorporation of noncanonical amino acids into fluorescent proteins in live cells. We will also discuss a noncanonical amino acid-containing fluorescent protein sensor that is based on a general protection-deprotection design strategy, for the selective detection and quantification of Hg2+.
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29
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Deng H, Yan S, Huang Y, Lei C, Nie Z. Design strategies for fluorescent proteins/mimics and their applications in biosensing and bioimaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Xu F, Fan M, Kang S, Duan X. A genetically encoded fluorescent biosensor for detecting nitroreductase activity in living cancer cells. Anal Chim Acta 2019; 1088:131-136. [DOI: 10.1016/j.aca.2019.08.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/16/2019] [Accepted: 08/25/2019] [Indexed: 01/19/2023]
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31
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Worthy HL, Auhim HS, Jamieson WD, Pope JR, Wall A, Batchelor R, Johnson RL, Watkins DW, Rizkallah P, Castell OK, Jones DD. Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry. Commun Chem 2019. [DOI: 10.1038/s42004-019-0185-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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32
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Lieser RM, Chen W, Sullivan MO. Controlled Epidermal Growth Factor Receptor Ligand Display on Cancer Suicide Enzymes via Unnatural Amino Acid Engineering for Enhanced Intracellular Delivery in Breast Cancer Cells. Bioconjug Chem 2019; 30:432-442. [PMID: 30615416 DOI: 10.1021/acs.bioconjchem.8b00783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are ideal candidates for disease treatment because of their high specificity and potency. Despite this potential, delivery of proteins remains a significant challenge due to the intrinsic size, charge, and stability of proteins. Attempts to overcome these challenges have most commonly relied on direct conjugation of polymers and peptides to proteins via reactive groups on naturally occurring residues. While such approaches have shown some success, they allow limited control of the spacing and number of moieties coupled to proteins, which can hinder bioactivity and delivery capabilities of the therapeutic. Here, we describe a strategy to site-specifically conjugate delivery moieties to therapeutic proteins through unnatural amino acid (UAA) incorporation, in order to explore the effect of epidermal growth factor receptor (EGFR)-targeted ligand valency and spacing on internalization of proteins in EGFR-overexpressing inflammatory breast cancer (IBC) cells. Our results demonstrate the ability to enhance targeted protein delivery by tuning a small number of EGFR ligands per protein and clustering these ligands to promote multivalent ligand-receptor interactions. Furthermore, the tailorability of this simple approach was demonstrated through IBC-targeted cell death via the delivery of yeast cytosine deaminase (yCD), a prodrug converting enzyme.
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Affiliation(s)
- Rachel M Lieser
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
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33
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Wang L, Chen X, Guo X, Li J, Liu Q, Kang F, Wang X, Hu C, Liu H, Gong W, Zhuang W, Liu X, Wang J. Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion. BIOPHYSICS REPORTS 2018; 4:273-285. [PMID: 30533492 PMCID: PMC6245237 DOI: 10.1007/s41048-018-0073-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/17/2018] [Indexed: 11/11/2022] Open
Abstract
ABSTRACT Fluorescent proteins (FPs) with emission wavelengths in the far-red and infrared regions of the spectrum provide powerful tools for deep-tissue and super-resolution imaging. The development of red-shifted FPs has evoked widespread interest and continuous engineering efforts. In this article, based on a computational design and genetic code expansion, we report a rational approach to significantly expand and red-shift the chromophore of green fluorescent protein (GFP). We applied computational calculations to predict the excitation and emission wavelengths of a FP chromophore harboring unnatural amino acids (UAA) and identify in silico an appropriate UAA, 2-amino-3-(6-hydroxynaphthalen-2-yl)propanoic acid (naphthol-Ala). Our methodology allowed us to formulate a GFP variant (cpsfGFP-66-Naphthol-Ala) with red-shifted absorbance and emission spectral maxima exceeding 60 and 130 nm, respectively, compared to those of GFP. The GFP chromophore is formed through autocatalytic post-translational modification to generate a planar 4-(p-hydroxybenzylidene)-5-imidazolinone chromophore. We solved the crystal structure of cpsfGFP-66-naphthol-Ala at 1.3 Å resolution and demonstrated the formation of a much larger conjugated π-system when the phenol group is replaced by naphthol. These results explain the significant red-shifting of the excitation and emission spectra of cpsfGFP-66-naphthol-Ala. GRAPHICAL ABSTRACT
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Affiliation(s)
- Li Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University, Changchun, 130012 China
| | - Xuzhen Guo
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jiasong Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qi Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fuying Kang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xudong Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Cheng Hu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Haiping Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Weimin Gong
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002 China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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34
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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35
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Novel alanines bearing a heteroaromatic side chain: synthesis and studies on fluorescent chemosensing of metal cations with biological relevance. Amino Acids 2018. [DOI: 10.1007/s00726-018-2549-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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36
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Ferreira RCM, M. Raposo MM, Costa SPG. Heterocyclic amino acids as fluorescent reporters for transition metals: synthesis and evaluation of novel furyl-benzoxazol-5-yl-l-alanines. NEW J CHEM 2018. [DOI: 10.1039/c7nj04459c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel benzoxazol-5-yl-l-alanines with heterocyclic pendants were synthesized and investigated as fluorescent reporters for metal cations through spectrofluorimetric titrations.
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37
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Shang X, Wang N, Cerny R, Niu W, Guo J. Fluorescent Protein-Based Turn-On Probe through a General Protection-Deprotection Design Strategy. ACS Sens 2017; 2:961-966. [PMID: 28750537 DOI: 10.1021/acssensors.7b00223] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrated a general protection-deprotection strategy for the design of fluorescent protein biosensors through the construction of a turn-on Hg2+ sensor. A combination of fluorescent protein engineering and unnatural amino acid mutagenesis was used. Unlike previously reported fluorescent protein-based Hg2+ sensors that relied on the binding of Hg2+ to the sulfhydryl group of cysteine residues, a well-established chemical reaction, oxymercuration, was transformed into biological format and incorporated into our sensor design. This novel Hg2+ sensor displayed good sensitivity and selectivity both in vitro and in live bacterial cells. Over 60-fold change in fluorescence signal output was observed in the presence of 10 μM Hg2+, while such a change was undetectable when nine other metal ions were tested. This new design strategy could expand the repertoire of fluorescent protein-based biosensors for the detection of small-molecule analytes.
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Affiliation(s)
- Xin Shang
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Nanxi Wang
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ronald Cerny
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry and ‡Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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38
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Villa JK, Tran HA, Vipani M, Gianturco S, Bhasin K, Russell BL, Harbron EJ, Young DD. Fluorescence Modulation of Green Fluorescent Protein Using Fluorinated Unnatural Amino Acids. Molecules 2017; 22:molecules22071194. [PMID: 28714902 PMCID: PMC5806519 DOI: 10.3390/molecules22071194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/28/2022] Open
Abstract
The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore. Relative to wild type GFP, the fluorescence spectrum of the protein is altered with each additional fluorine atom, and the mutant GFPs have the potential to be employed as pH sensors due to the altered electronic properties of the fluorine atoms.
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Affiliation(s)
- Jordan K Villa
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Hong-Anh Tran
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Megha Vipani
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Stephanie Gianturco
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Konark Bhasin
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Brent L Russell
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Elizabeth J Harbron
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
| | - Douglas D Young
- Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.
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39
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Wang N, Yuan Z, Niu W, Li Q, Guo J. Synthetic biology approach for the development of conditionally replicating HIV-1 vaccine. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2017; 92:455-462. [PMID: 28983143 PMCID: PMC5624719 DOI: 10.1002/jctb.5174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While the combined antiretroviral therapy has resulted in a significant decrease in HIV-1 related morbidity and mortality, the HIV-1 pandemic has not been substantially averted. To curtail the 2.4 million new infections each year, a prophylactic HIV-1 vaccine is urgently needed. This review first summarizes four major completed clinical efficacy trials of prophylactic HIV-1 vaccine and their outcomes. Next, it discusses several other approaches that have not yet advanced to clinical efficacy trials, but provided valuable insights into vaccine design. Among them, live-attenuated vaccines (LAVs) provided excellent protection in a non-human primate model. However, safety concerns have precluded the current version of LAVs from clinical application. As the major component of this review, two synthetic biology approaches for improving the safety of HIV-1 LAVs through controlling HIV-1 replication are discussed. Particular focus is on a novel approach that uses unnatural amino acid-mediated suppression of amber nonsense codon to generate conditionally replicating HIV-1 variants. The objective is to attract more attention towards this promising research field and to provoke creative designs and innovative utilization of the two control strategies.
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Affiliation(s)
- Nanxi Wang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Zhe Yuan
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Qingsheng Li
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
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40
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Abstract
Fluorescent proteins of different colors are useful probes to study protein structure and function, and to investigate cellular events and conditions. Large efforts have focused on engineering new properties into fluorescent proteins via rational design and directed evolution. In addition to applications in imaging of protein expression level and subcellular localization, fluorescent proteins have been increasingly engineered to act as biosensors to track concentrations of small-molecule metabolites, enzyme activities, and protein conformational changes in living cells. Unlike small-molecule fluorescence biosensors, fluorescent proteins are genetically encodable, and thus can be expressed inside living cells. Attachment of organelle-specific signals to the proteins allows their localization to be specified. Recently, a new class of fluorescent protein biosensors has been developed to include unnatural amino acids as the sensing element. The unique chemical and physical properties of the unnatural amino acids enable sensor designs that cannot be realized by using the standard genetic code with the 20 canonical amino acids. In this chapter, we detail the general procedure for the genetic incorporation of unnatural amino acids. We further present two protocols for the in vitro and in vivo detection of hydrogen peroxide (H2O2) using a fluorescent protein biosensor that contains an unnatural amino acid, p-boronophenylalanine.
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Affiliation(s)
- Wei Niu
- University of Nebraska-Lincoln, Lincoln, NE, United States.
| | - Jiantao Guo
- University of Nebraska-Lincoln, Lincoln, NE, United States.
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41
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Non-canonical amino acids bearing thiophene and bithiophene: synthesis by an Ugi multicomponent reaction and studies on ion recognition ability. Amino Acids 2017; 49:921-930. [DOI: 10.1007/s00726-017-2392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 02/01/2017] [Indexed: 01/11/2023]
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42
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Xiao H, Schultz PG. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023945. [PMID: 27413101 DOI: 10.1101/cshperspect.a023945] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.
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Affiliation(s)
- Han Xiao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 California Institute for Biomedical Research, La Jolla, California 92037
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Hartley AM, Worthy HL, Reddington SC, Rizkallah PJ, Jones DD. Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle. Chem Sci 2016; 7:6484-6491. [PMID: 28451106 PMCID: PMC5355941 DOI: 10.1039/c6sc00944a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/28/2016] [Indexed: 01/15/2023] Open
Abstract
Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation.
Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-l-phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the phenyl azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded phenyl azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks.
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Affiliation(s)
| | | | | | | | - D Dafydd Jones
- School of Biosciences , Cardiff University , Cardiff , UK .
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44
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Wang N, Shang X, Cerny R, Niu W, Guo J. Systematic Evolution and Study of UAGN Decoding tRNAs in a Genomically Recoded Bacteria. Sci Rep 2016; 6:21898. [PMID: 26906548 PMCID: PMC4764823 DOI: 10.1038/srep21898] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
We report the first systematic evolution and study of tRNA variants that are able to read a set of UAGN (N = A, G, U, C) codons in a genomically recoded E. coli strain that lacks any endogenous in-frame UAGN sequences and release factor 1. Through randomizing bases in anticodon stem-loop followed by a functional selection, we identified tRNA mutants with significantly improved UAGN decoding efficiency, which will augment the current efforts on genetic code expansion through quadruplet decoding. We found that an extended anticodon loop with an extra nucleotide was required for a detectable efficiency in UAGN decoding. We also observed that this crucial extra nucleotide was converged to a U (position 33.5) in all of the top tRNA hits no matter which UAGN codon they suppress. The insertion of U33.5 in the anticodon loop likely causes tRNA distortion and affects anticodon-codon interaction, which induces +1 frameshift in the P site of ribosome. A new model was proposed to explain the observed features of UAGN decoding. Overall, our findings elevate our understanding of the +1 frameshift mechanism and provide a useful guidance for further efforts on the genetic code expansion using a non-canonical quadruplet reading frame.
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Affiliation(s)
- Nanxi Wang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Xin Shang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Ronald Cerny
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Wei Niu
- Department of Chemical &Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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45
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Dippel AB, Olenginski GM, Maurici N, Liskov MT, Brewer SH, Phillips-Piro CM. Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study. Acta Crystallogr D Struct Biol 2016; 72:121-30. [PMID: 26894540 PMCID: PMC4756619 DOI: 10.1107/s2059798315022858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/29/2015] [Indexed: 11/10/2022] Open
Abstract
The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolution and permit a direct correlation between the structure and spectroscopic data to be made. The structural implications were quantified by comparing the root-mean-square deviation (r.m.s.d.) between the crystal structure of wild-type sfGFP and the protein constructs containing either pCNF or pCCF in the local environment around the UAAs and in the overall protein structure. The results suggest that the selective placement of these spectroscopic reporter UAAs permits local protein environments to be studied in a relatively nonperturbative fashion with site-specificity.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Gregory M. Olenginski
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Nicole Maurici
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Melanie T. Liskov
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
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46
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Lampkowski JS, Uthappa DM, Young DD. Site-specific incorporation of a fluorescent terphenyl unnatural amino acid. Bioorg Med Chem Lett 2015; 25:5277-80. [PMID: 26421994 DOI: 10.1016/j.bmcl.2015.09.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/16/2015] [Accepted: 09/21/2015] [Indexed: 11/26/2022]
Abstract
The site-specific incorporation of unnatural amino acids into proteins has a wide range of biological implications. Of particular interest is the incorporation of fluorescent probes as a mechanism to track protein function, transport, and folding. Thus, the development of a novel system for the incorporation of new fluorescent unnatural amino acids has significant utility. Specifically, we have elucidated an aminoacyl-tRNA synthetase capable of recognizing a terphenyl UAA derivative, and charging a cognate tRNA with this amino acid for protein incorporation. Moreover, we have successfully incorporated this fluorescent UAA into GFP at several key residues, demonstrating a novel means to modulate fluorescence within the protein.
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Affiliation(s)
| | - Diya M Uthappa
- Department of Chemistry, College of William & Mary, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, Williamsburg, VA 23187, USA
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47
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Synthesis of fluorescent d-amino acids with 4-acetamidobiphenyl and 4-N,N-dimethylamino-1,8-naphthalimido containing side chains. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.06.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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Wang N, Ju T, Niu W, Guo J. Fine-tuning interaction between aminoacyl-tRNA synthetase and tRNA for efficient synthesis of proteins containing unnatural amino acids. ACS Synth Biol 2015; 4:207-12. [PMID: 24847685 PMCID: PMC4384836 DOI: 10.1021/sb500195w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
By
using a directed evolution approach, we have identified aminoacyl-tRNA
synthetase variants with significantly enhanced activity for the incorporation
of unnatural amino acids into proteins in response to the amber nonsense
codon in bacteria. We demonstrated that the optimization of anticodon
recognition of tRNA by aminoacyl-tRNA synthetase led to improved incorporation
efficiency that is unnatural amino acid-specific. The findings will
facilitate the creation of an optimized system for the genetic incorporation
of unnatural amino acids in bacteria.
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Affiliation(s)
- Nanxi Wang
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Tong Ju
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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49
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Reddington SC, Driezis S, Hartley AM, Watson PD, Rizkallah PJ, Jones DD. Genetically encoded phenyl azide photochemistry drives positive and negative functional modulation of a red fluorescent protein. RSC Adv 2015. [DOI: 10.1039/c5ra13552d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genetically encoded incorporation of phenyl azide chemistry into the autofluorescent protein mCherry can be used to switch on or off fluorescence.
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50
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Tamura T, Hamachi I. Recent progress in design of protein-based fluorescent biosensors and their cellular applications. ACS Chem Biol 2014; 9:2708-17. [PMID: 25317665 DOI: 10.1021/cb500661v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based fluorescent biosensors have emerged as key bioanalytical tools to visualize and quantify a wide range of biological substances and events in vitro, in cells, and even in vivo. On the basis of the construction method, the protein-based fluorescent biosensors can be principally classified into two classes: (1) genetically encoded fluorescent biosensors harnessing fluorescent proteins (FPs) and (2) semisynthetic biosensors comprised of protein scaffolds and synthetic fluorophores. Recent advances in protein engineering and chemical biology not only allowed the further optimization of conventional biosensors but also facilitated the creation of novel biosensors based on unique strategies. In this review, we survey the recent studies in the development and improvement of protein-based fluorescent biosensors and highlight the successful applications to live cell and in vivo imaging. Furthermore, we provide perspectives on possible future directions of the technique.
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Affiliation(s)
- Tomonori Tamura
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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