Noncanonical amino acids in the interrogation of cellular protein synthesis

Proteins in living cells can be made receptive to bioorthogonal chemistries through metabolic labeling with appropriately designed noncanonical amino acids (ncAAs). In the simplest approach to metabolic labeling, an amino acid analog replaces one of the natural amino acids specified by the protein's gene (or genes) of interest. Through manipulation of experimental conditions, the extent of the replacement can be adjusted. This approach, often termed residue-specific incorporation, allows the ncAA to be incorporated in controlled proportions into positions normally occupied by the natural amino acid residue. For a protein to be labeled in this way with an ncAA, it must fulfill just two requirements: (i) the corresponding natural amino acid must be encoded within the sequence of the protein at the genetic level, and (ii) the protein must be expressed while the ncAA is in the cell. Because this approach permits labeling of proteins throughout the cell, it has enabled us to develop strategies to track cellular protein synthesis by tagging proteins with reactive ncAAs. In procedures similar to isotopic labeling, translationally active ncAAs are incorporated into proteins during a "pulse" in which newly synthesized proteins are tagged. The set of tagged proteins can be distinguished from those made before the pulse by bioorthogonally ligating the ncAA side chain to probes that permit detection, isolation, and visualization of the labeled proteins. Noncanonical amino acids with side chains containing azide, alkyne, or alkene groups have been especially useful in experiments of this kind. They have been incorporated into proteins in the form of methionine analogs that are substrates for the natural translational machinery. The selectivity of the method can be enhanced through the use of mutant aminoacyl tRNA synthetases (aaRSs) that permit incorporation of ncAAs not used by the endogenous biomachinery. Through expression of mutant aaRSs, proteins can be tagged with other useful ncAAs, including analogs that contain ketones or aryl halides. High-throughput screening strategies can identify aaRS variants that activate a wide range of ncAAs. Controlled expression of mutant synthetases has been combined with ncAA tagging to permit cell-selective metabolic labeling of proteins. Expression of a mutant synthetase in a portion of cells within a complex cellular mixture restricts labeling to that subset of cells. Proteins synthesized in cells not expressing the synthetase are neither labeled nor detected. In multicellular environments, this approach permits the identification of the cellular origins of labeled proteins. In this Account, we summarize the tools and strategies that have been developed for interrogating cellular protein synthesis through residue-specific tagging with ncAAs. We describe the chemical and genetic components of ncAA-tagging strategies and discuss how these methods are being used in chemical biology.     

Site‐Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin

Expansion of the structural diversity of peptide antibiotics was performed through two different methods. Supplementation‐based incorporation (SPI) and stop‐codon suppression (SCS) approaches were used for co‐translational incorporation of isostructural and orthogonal noncanonical amino acids (ncAAs) into the lasso peptide capistruin. Two ncAAs were employed for the SPI method and five for the SCS method; each of them probing the incorporation of ncAAs in strategic positions of the molecule. Evaluation of the assembly by HR‐ESI‐MS proved more successful for the SCS method. Bio‐orthogonal chemistry was used for post‐biosynthetic modification of capistruin congener Cap_Alk10 containing the ncAA Alk (Nε‐Alloc‐L ‐lysine) instead of Ala. A second‐generation Hoveyda–Grubbs catalyst was used for an in vitro metathesis reaction with Cap_Alk10 and an allyl alcohol, which offers options for post‐biosynthetic modifications. The use of synthetic biology allows for the in vivo production of new peptide‐based antibiotics from an expanded amino acid repertoire.     

Development of Multivalent Conjugates with a Single Non-Canonical Amino Acid

Proteins represent powerful biomacromolecules due to their unique functionality and broad utility both in the cell and in non-biological applications. The genetic encoding of non-canonical amino acids (ncAAs) facilitates functional diversification of these already powerful proteins. Specifically, ncAAs have been demonstrated to provide unique functional handles to bioorthogonally introduce novel functionality via conjugation reactions. Herein we examine the ability of a single ncAA to serve as a handle to generate multivalent bioconjugates to introduce two or more additional components to a protein, yielding a multivalent conjugate. To accomplish this aim, p-bromopropargyloxyphenyalanine (pBrPrF) was genetically encoded into both superfolder green fluorescent protein (sfGFP) and ubiquitin model proteins to serve as a conjugation handle. A sequential bioconjugation sequence involving a copper-assisted cycloaddition reaction coupled with a subsequent Sonogashira cross-coupling was then optimized. The linkage of two additional molecules to the model protein via these reactions yielded the desired multivalent bioconjugate. This domino approach using a single ncAA has a plethora of applications in both therapeutics and diagnostics as multiple unique moieties can be introduced into proteins in a highly controlled fashion.     

Two‐Tier Screening Platform for Directed Evolution of Aminoacyl–tRNA Synthetases with Enhanced Stop Codon Suppression Efficiency

Genetic code expansion through amber stop codon suppression provides a powerful tool for introducing non‐proteinogenic functionalities into proteins for a broad range of applications. However, ribosomal incorporation of noncanonical amino acids (ncAAs) by means of engineered aminoacyl–tRNA synthetases (aaRSs) often proceeds with significantly reduced efficiency compared to sense codon translation. Here, we report the implementation of a versatile platform for the development of engineered aaRSs with enhanced efficiency in mediating ncAA incorporation by amber stop codon suppression. This system integrates a white/blue colony screen with a plate‐based colorimetric assay, thereby combining high‐throughput capabilities with reliable and quantitative measurement of aaRS‐dependent ncAA incorporation efficiency. This two‐tier functional screening system was successfully applied to obtain a pyrrolysyl–tRNA synthetase (PylRS) variant (CrtK‐RS(4.1)) with significantly improved efficiency (+250–370 %) for mediating the incorporation of N^?‐crotonyl‐lysine and other lysine analogues of relevance for the study of protein post‐translational modifications into a target protein. Interestingly, the beneficial mutations accumulated by CrtK‐RS(4.1) were found to localize within the noncatalytic N‐terminal domain of the enzyme and could be transferred to another PylRS variant, improving the ability of the variant to incorporate its corresponding ncAA substrate. This work introduces an efficient platform for the improvement of aaRSs that could be readily extended to other members of this enzyme family and/or other target ncAAs.     

Selection,Addiction and Catalysis: Emerging Trends for the Incorporation of Noncanonical Amino Acids into Peptides and Proteins in Vivo

Expanding the genetic code of organisms by incorporating noncanonical amino acids (ncAAs) into target proteins through the suppression of stop codons in vivo has profoundly impacted how we perform protein modification or detect proteins and their interaction partners in their native environment. Yet, with genetic code expansion strategies maturing over the past 15 years, new applications that make use—or indeed repurpose—these techniques are beginning to emerge. This Concept article highlights three of these developments: 1) The incorporation of ncAAs for the biosynthesis and selection of bioactive macrocyclic peptides with novel ring architectures, 2) synthetic biocontainment strategies based on the addiction of microorganisms to ncAAs, and 3) enzyme design strategies, in which ncAAs with unique functionalities enable the catalysis of new-to-nature reactions. Key advances in all three areas are presented and potential future applications discussed.     

Micelle‐Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid‐Embedded Surface of a GPCR

Genetically encoded p‐azido‐phenylalanine (azF) residues in G protein‐coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne‐modified (DIBO‐modified) fluorescent probes by means of strain‐promoted [3+2] azide–alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent‐solubilized receptors exhibit up to 1000‐fold rate enhancement relative to azF residues on water‐exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle‐enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.     

SNAP‐Tag‐Based Subcellular Protein Labeling and Fluorescent Imaging with Naphthalimides

Genetically encoded technologies provide methods for the specific labeling and imaging of proteins, which is essential to understand the subcellular localization of these proteins and their function. Herein, we employed naphthalimide, an efficient two‐photon fluorophore, to develop O⁶‐benzylguanine (BG) derivatives for specific labeling of subcellular proteins and fluorescent imaging through the SNAP‐tag. Three naphthalimide–BG derivatives, TNI‐BG, QNI‐BG, and ONI‐BG, were conveniently synthesized through modular “click chemistry” in high yields. All of them showed high labeling efficiency with SNAP‐tag in solution (≈1–2×10³ s^?1 m ^?1) and in bacteria. Among them, ONI‐BG showed high specificity to diffused, histone H2B and mitochondria COX8A targeted SNAP‐tag in mammalian cells. The protein‐labeled naphthalimides exhibited high two‐photon absorption cross‐sections, which indicated their potential application in protein‐specific two‐photon fluorescent imaging, such as two‐photon fluorescent lifetime imaging and two‐photon multicolor imaging. Therefore, ONI‐BG is a versatile tool that can be used to track subcellular proteins through multiple fluorescent techniques.     

A Unique Genetically Encoded FRET Pair in Mammalian Cells

Förster resonance energy transfer (FRET) between two suitable fluorophores is a powerful tool to monitor dynamic changes in protein structure in vitro and in vivo. The ability to genetically encode a FRET pair represents a convenient “labeling‐free” strategy to incorporate them into target protein(s). Currently, the only genetically encoded FRET pairs available for use in mammalian cells use fluorescent proteins. However, their large size can lead to unfavorable perturbations, particularly when two are used at the same time. Additionally, fluorescent proteins are largely restricted to a terminal attachment to the target, which might not be optimal. Here, we report the development of an alternative genetically encoded FRET pair in mammalian cells that circumvents these challenges by taking advantage of a small genetically encoded fluorescent unnatural amino acid as the donor and enhanced green fluorescent protein (EGFP) as the acceptor. The small size of Anap relative to fluorescent proteins, and the ability to co‐translationally incorporate it into internal sites on the target protein, endows this novel FRET pair with improved versatility over its counterparts that rely upon two fluorescent proteins.     

Recent Developments of Engineered Translational Machineries for the Incorporation of Non-Canonical Amino Acids into Polypeptides

Genetic code expansion and reprogramming methodologies allow us to incorporate non-canonical amino acids (ncAAs) bearing various functional groups, such as fluorescent groups, bioorthogonal functional groups, and post-translational modifications, into a desired position or multiple positions in polypeptides both in vitro and in vivo. In order to efficiently incorporate a wide range of ncAAs, several methodologies have been developed, such as orthogonal aminoacyl-tRNA-synthetase (AARS)–tRNA pairs, aminoacylation ribozymes, frame-shift suppression of quadruplet codons, and engineered ribosomes. More recently, it has been reported that an engineered translation system specifically utilizes an artificially built genetic code and functions orthogonally to naturally occurring counterpart. In this review we summarize recent advances in the field of ribosomal polypeptide synthesis containing ncAAs.     

Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria

Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment – typically at a single site or at a few sites per protein – of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l -phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production – using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain – of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.     

DNA Primer Extension with Cyclopropenylated 7‐Deaza‐2′‐deoxyadenosine and Efficient Bioorthogonal Labeling in Vitro and in Living Cells

A deoxyadenosine triphosphate (dATP) analogue for DNA labeling was synthesized with the 1‐methylcyclopropene (1MCP) group at the 7‐position of 7‐deaza‐2′‐deoxyadenosine and applied for primer extension experiments. The real‐time kinetic data reveals that this 1MCP‐modified dATP analogue is incorporated into DNA much faster than that of the similarly 1MCP‐modified deoxyuridine triphosphate (dUTP) analogue. The postsynthetic fluorescent labeling of these oligonucleotides works efficiently according to PAGE analysis, and can be applied for immobilization of a functional antibody on a surface. Site‐specific labeling at two different positions in DNA was achieved and the bioorthogonality of the postsynthetic fluorescent labeling was demonstrated in living HeLa cells.     

TiO2/TNO homojunction introduced in a dye‐sensitized solar cell with a novel TNO transparent conductive oxide film

In this study, niobium‐doped titanium oxide (TNO) was employed for a novel transparent conductive oxide (TCO) film to construct a porous‐TiO₂/TNO homojunction in a dye‐sensitized solar cell (DSSC). However, considering a balance between the electrical and optical properties of the TCO film, the sheet resistance in TNO was tuned to be higher than that in a typical fluorine‐doped tin oxide (FTO). The photovoltaic performance of the cell with the TNO film (TNO cell) was optimized to be almost comparable to that with a conventional FTO film (FTO cell) by coating the surface of the porous‐TiO₂ layer with a thin alumina or magnesia film to block a back reaction within the cell. An electrochemical impedance measurement was conducted to determine the detailed photovoltaic performance from the viewpoint of electron transportation in the cell. R₁, the real part of ω₁, indicated that electron transportation at the porous‐TiO₂/TNO interface was more favorable than that at the porous‐TiO₂/FTO interface, which was supported by AC phase change in the cell at a high‐frequency range. We found that the homojunction newly introduced in the cell is one of the key concepts for developing a DSSC into a high‐performance photovoltaic device.     

Hairy fluorescent nanoparticles from one‐pot click chemistry and atom transfer radical emulsion polymerization

Well‐defined hairy and crosslinked fluorescent nanoparticles with diameters in the range 70–220 nm were obtained from simultaneous copper‐catalyzed alkyne–azide cycloaddition (CuAAC) and atom transfer radical emulsion polymerization (ATREP) of a mixture of styrene, divinylbenzene, 4‐vinylbenzylazide and 7‐propinyloxycoumarin (Cr), using bromide‐terminated poly(ethylene glycol) (PEG) as macroinitiator, Tween‐20 as emulsifier, copper(I) bromide as catalyst and pentamethyldiethylenetriamine as ligand. The generation of biocompatible PEG brushes and the introduction of fluorescent functionalities as well as crosslinking of nanoparticles were realized in one step. In order to verify that functionalization and propagation of polymer chains could be realized in a controlled manner by one‐pot simultaneous ATREP and CuAAC, linear block copolymers of PEG and polystyrene (PS) with partially clicked pendent Cr groups (PEG‐b‐(PS‐c‐Cr)) were synthesized. All prepared PEG‐b‐(PS‐c‐Cr) copolymers had a controlled molecular weight and defined molecular structure. The hairy fluorescent nanoparticles exhibit a low cytotoxicity and could find applications in cell labeling. © 2013 Society of Chemical Industry     

Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology

Fluorescence spectroscopy is a powerful tool for probing complex biological processes. The ubiquity of peptide–protein and protein–protein interactions in these processes has made them important targets for fluorescence labeling, and to allow sensitive readout of information concerning location, interactions with other biomolecules, and macromolecular dynamics. This review describes recent advances in design, properties and applications in the area of fluorescent amino acids (FlAAs). The ability to site‐selectively incorporate fluorescent amino acid building blocks into a protein or peptide of interest provides the advantage of closely retaining native function and appearance. The development of an array of fluorescent amino acids with a variety of properties, such as environment sensitivity, chelation‐enhanced fluorescence, and profluorescence, has allowed researchers to gain insights into biological processes, including protein conformational changes, binding events, enzyme activities, and protein trafficking and localization.     

Mutation of Conserved Residues Increases in Vitro Activity of the Formylglycine‐Generating Enzyme

The formylglycine‐generating enzyme (FGE) recognizes proteins with a specific cysteine‐containing six‐amino‐acid motif and converts this cysteine residue into formylglycine. The resulting aldehyde function provides a unique handle for selective protein labeling. We have identified two mutations in FGE from Thermomonospora curvata that increase this catalytic efficiency more than 40‐fold. The resulting activity and stability, as well as its ease of recombinant production, make this FGE variant a practical reagent for in vitro protein engineering.     

Genetically Encoded Biotin Analogues: Incorporation and Application in Bacterial and Mammalian Cells

The biotin–streptavidin interaction is among the strongest known in nature. Herein, the site-directed incorporation of biotin and 2-iminobiotin composed of noncanonical amino acids (ncAAs) into proteins is reported. 2-Iminobiotin lysine was employed for protein purification based on the pH-dependent dissociation constant to streptavidin. By using the high-affinity binding of biotin lysine, the bacterial protein RecA could be specifically isolated and its interaction partners analyzed. Furthermore, the biotinylation approach was successfully transferred to mammalian cells. Stringent control over the biotinylation site and the tunable affinity between ncAAs and streptavidin of the different biotin analogues make this approach an attractive tool for protein interaction studies, protein immobilization, and the generation of well-defined protein–drug conjugates.     

Recent Progress in Strategies for the Creation of Protein‐Based Fluorescent Biosensors

The creation of novel bioanalytical tools for the detection and monitoring of a range of important target substances and biological events in vivo and in vitro is a great challenge in chemical biology and biotechnology. Protein‐based fluorescent biosensors—integrated devices that convert a molecular‐recognition event to a fluorescent signal—have recently emerged as a powerful tool. As the recognition units various proteins that can specifically recognize and bind a variety of molecules of biological significance with high affinity are employed. For the transducer, fluorescent proteins, such as green fluorescent protein (GFP) or synthetic fluorophores, are mostly adopted. Recent progress in protein engineering and organic synthesis allows us to manipulate proteins genetically and/or chemically, and a library of such protein scaffolds has been significantly expanded by genome projects. In this review, we briefly describe the recent progress of protein‐based fluorescent biosensors on the basis of their platform and construction strategy, which are primarily divided into the genetically encoded fluorescent biosensors and chemically constructed biosensors.     

Preparation of thermoresponsive fluorescent carbon dots for cellular imaging

Nowadays, carbon dots (CDs ) have aroused widespread interest due to their chemical stability, biocompatibility as well as low toxicity. Herein, polymerizable CD monomers were synthesized through amidation between hydrophobic CDs and methacryloyl chloride, which has emerged as a facile method for preparing various fluorescent CD monomers. The fluorescent polymerizable CDs were copolymerized with N‐ isopropylacrylamide (NIPAM ) to form thermoresponsive fluorescent nanoparticles. The poly(NIPAM ) (PNIPAM ) grafted hydrophobic CDs (CDs ‐g ‐PNIPAM ) have excellent dispersivity in water, rendering hydrophobic CDs with fluorescence properties in aqueous media. Moreover, CDs ‐g ‐PNIPAM nanocomposites show a remarkable thermoresponsive behavior, and the fluorescence intensity decreases progressively with increase in temperature. Cytotoxicity tests show that CDs ‐g ‐PNIPAM nanocomposites have great biocompatibility. When the CDs ‐g ‐PNIPAM nanocomposites were cultured with HaCaT cells at a concentration of 2000 µg mL ^?1, cell viability was maintained over 85%. Benefiting from the copolymerization of NIPAM , the excitation‐independent fluorescence of CDs ‐g ‐PNIPAM nanocomposites can be used for cellular labeling and show long‐term biostability in a cellular environment. © 2016 Society of Chemical Industry     

Structure and morphology of nanoporous zno and dark current‐Voltage characteristics of the glass/(TCO)/zno/poly[2,7‐(9,9‐dioctylfluorene)‐alt‐(5,5'‐bithiophene)/ag structure

The hybrid organic‐inorganic structure based on glass/(TCO)/nanoporous ZnO/poly[2,7‐(9,9‐dioctylfluorene)‐alt‐(5,5′‐bithiophene)]/Ag that was prepared by physical deposition has been investigated. The structure of the nanostructured ZnO obtained by magnetron sputtering was confirmed by X‐ray diffractometry (XRD) and energy dispersive X‐ray spectroscopy (EDX). Scanning electron microscopy (SEM) analysis proved the existence of short and interconnected zinc oxide (ZnO) fibers, which form a continuous porous network with pores having an average diameter of 100 nm. Current‐voltage (I‐V) curves of the glass/TCO/ZnO/PF‐BT/Ag hybrid structure are similar to those of typical p‐n junctions and stable until 90°C temperature. According to the I‐V characteristics, the dominant mechanism of current flow is based on the generation‐recombination of carriers in the depletion region at low direct biases and also on the injection of carriers at high biases. The reverse branch of the I‐V characteristic, calculated in log‐log scale, shows one segment with a power coefficient of 3/2 at room temperature. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 42415.     

Microfluidic assembly of uniform fluorescent microbeads from quantum‐dot‐loaded fluorine‐containing microemulsion

We report a facile strategy for fabricating fluorescent quantum dot (QD)‐loaded microbeads by means of microfluidic technology. First, a functional fluorine‐containing microemulsion was synthesized with poly[(2‐(N‐ethylperfluorobutanesulfonamido)ethyl acrylate)‐co‐(methyl methacrylate)‐co‐(butyl acrylate)] (poly(FBMA‐co‐MMA‐co‐BA)) as the core and glycidyl methacrylate (GMA) as the shell via differential microemulsion polymerization. Then, CdTe QDs capped with N‐acetyl‐l ‐cysteine (NAC) were assembled into the poly(FBMA‐co‐MMA‐co‐BA‐co‐GMA) microemulsion particles through the reaction of the epoxy group on the shell of the microemulsion and the carboxyl group of the NAC ligand capped on the QDs. Finally, fluorescent microbeads were fabricated using the CdTe QD‐loaded fluorine‐containing microemulsion as the discontinuous phase and methylsilicone oil as the continuous phase by means of a simple microfluidic device. By changing flow rate of methylsilicone oil and hybrid microemulsion system, fluorescent microbeads with adjustable sizes ranging from 290 to 420 µm were achieved. The morphology and fluorescent properties of the microbeads were thoroughly investigated using optical microscopy and fluorescence microscopy. Results showed that the fluorescent microbeads exhibited uniform size distribution and excellent fluorescence performance. © 2014 Society of Chemical Industry