Genetic Code Expansion: A Brief History and Perspective

Reversible Protein Labeling via Genetically Encoded Dithiolane-Containing Amino Acid and Organoarsenic Probes

Conventional protein labeling techniques often rely on irreversible covalent bonds, limiting dynamic control over protein modifications. Here, we present a reversible protein labeling strategy using genetically encoded dithiolane-containing amino acid (dtF) and organoarsenic conjugation chemistry. Using dithiarsolane dicarboxylic acid probe A2, we achieved near-quantitative labeling and ethanedithiol-mediated removal within 1 h at room temperature. A2 exhibited reduced toxicity with a 7-fold higher IC50 compared to arsenoxide, and its fluorescent derivative A2-FB showed no cytotoxicity up to 100 μM, enabling live-cell applications. This is the first demonstration of dithiol-arsenic chemistry at a single amino acid residue, providing a structural alternative to dicysteine motifs. Reversible labeling was validated in purified proteins (sfGFP-Y151dtF and MYO-K99dtF) and live Escherichia coli, offering a versatile tool for dynamic protein modifications and molecular tracking in biological systems.

Streamlining tRNA-Synthetase Evolution for Genetic Code Expansion and Deep Sequencing Analyses of Its Evolved Variants

Proteins are typically composed of 20 amino acids encoded by 61 codons. However, some bacteria and archaea have evolved to incorporate additional amino acids by repurposing stop codons, a phenomenon that led to the development of genetic code expansion (GCE) in the early 21st century. This approach introduces orthogonal tRNA and aminoacyl-tRNA-synthetase (aaRS) pairs into target organisms, enabling the incorporation of noncanonical amino acids (ncAAs) with distinct side chains into proteins. GCE has broad applications, including site-specific cross-linking, fluorescence labeling, and electron-transfer functionalities. Despite its versatility, improving the efficiency of ncAA incorporation remains a challenge. Directed evolution provides a powerful solution by introducing mutations into the aaRS sequence and applying selection to identify variants with enhanced activity. Here, we present a simplified directed evolution system designed to improve the activity of pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei. Our approach is accessible, requiring only basic laboratory equipment, making it suitable and facile to implement by graduate students. We evolved PylRS variants toward three distinct substrates, each pathway yielding unique, substrate-specific mutations. We characterized the impact of these mutations on both PylRS activity and expression levels, demonstrating that tandem codon randomization can be an effective strategy for improving PylRS function through additive effects of the mutations. Additionally, deep sequencing validated our approach, confirming its efficiency, revealing conserved and mutationally flexible sites and reinforcing the advantage of tandem mutations in PylRS evolution. Collectively, these findings streamline the process of evolving PylRS and provide insights into strategies for enhancing ncAA incorporation in synthetic biology and protein engineering.

Fluorescent labeling of proteins in vitro and in vivo using encoded peptide tags

Epitope tags are a simple and versatile way to label proteins as their sequences can easily be inserted into protein coding sequences, so that the expressed proteins will bear the tag(s). These tags can be used to identify and purify proteins in vitro using Western blots, flow cytometry, affinity chromatography, and other techniques. When labeled with a fluorescent probe, tagged proteins can be visualized in live or fixed cells or tissues using fluorescence microscopy, allowing for the study of protein dynamics. The most widely used epitope tags are those that have affinity to an antibody, which can be used in fixed-sample immunohistochemistry studies. While this will allow insight into a protein's localization, it will not provide any information on its dynamics. Other tags were developed with the intended use in live imaging. In this mini review, we discuss epitope tags that have affinity to antibodies, nanobodies, and small molecules and their use in fluorescence microscopy for fixed and live imaging.

Molecular process control for industrial biotechnology

The development of sustainable and economically competitive biotechnological processes is a central challenge of modern industrial biotechnology. Conventional strategies such as macroscopic and molecular bioprocess design are often insufficient to exploit their full potential. To circumvent this, molecular process control provides the missing link to further consolidate various optimization strategies to achieve multilayered process design. This review highlights the molecular mechanisms that can be exploited for molecular process control. These can either be endogenous or specifically implemented into the organism, and comprise regulatory mechanisms at the transcriptional, translational, and system levels. In addition to serving as a design tool to enhance existing bioprocesses, molecular process control is the gateway to biotechnological advances that will extend the boundaries of future process design.

Cell-free synthetic biology for natural product biosynthesis and discovery

Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.

Removing redundancy of the NCN codons in vitro for maximal sense codon reassignment

Expanding the genetic code affords exciting opportunities for synthetic biology, studies of protein function, and creation of diverse peptide libraries by mRNA display. Maximal expansion with the standard 64 codon code requires breaking the degeneracy of the 61 sense codons which encode for only 20 amino acids. In E. coli these 61 codons are decoded by 46 different tRNAs. Moreover, many codons are decoded by multiple tRNAs, further complicating efforts to break this redundancy. The overlapping decoding patterns of the 11 tRNAs in E. coli which read the 16 codons that encode serine, proline, threonine, and alanine codons exemplify this difficulty. Here we tackle this challenge by first outlining a general process to evaluate codons for their potential for reassignment. We then use this knowledge to assign these 16 codons to 10 different amino acids, more than doubling their encoding potential. Our work highlights the expanded potential of sense codon reassignment and points the way to a dramatically expanded code containing more than 30 monomers.

Noncanonical amino acids as prophage inducers for protein regulation in bacteria-based delivery systems

Genetically engineered bacteria represent a promising drug delivery tool for disease treatment. The development of new strategies for specific and independent protein regulation is necessary, especially for combination protein drug therapy. Using the well-studied Escherichia coli phage λ as a model system, we applied noncanonical amino acids (ncAAs) as novel inducers for protein regulation in a bacteria-based delivery system. Screening the permissive sites of the Cro protein revealed that incorporation of AlocK at the K8 site with the MbPylRS-349F/tRNAPyl system produced a functional Cro-K8AlocK variant. Using an engineered λ lysogen expressing the MbPylRS-349F/tRNAPyl pair, Cro-8X, and the reporter mNeonGreen, in vitro and in vivo experiments showed that AlocK led to bacterial lysis through prophage activation and the release of mNeonGreen. If mNeonGreen was integrated into the λ prophage genome, λ phages released due to AlocK induction delivered the reporter gene into the recipient E. coli strain, enabling mNeonGreen expression. Furthermore, insertion of pIF at the F14 site with the AfpIFRS/tRNATyr pair produced a functional Cro-F14pIF variant. Importantly, AfpIFRS/tRNATyr and MbPylRS-349F/tRNAPyl pairs were confirmed to be mutually orthogonal. In a mixture of two engineered λ lysogens expressing different aaRS/tRNAs, Cro-ncAAs, and reporter proteins, AlocK and pIF independently induced bacterial lysis and activated the expression of mNeonGreen and mCherry in the recipient E. coli strain. Collectively, the proposed bacteria-based delivery system provides two options for protein delivery and enables independent regulation of multiple proteins with ncAAs, offering a novel approach for in situ protein regulation and combination therapy.

IMPORTANCE

The use of genetically engineered bacteria as drug delivery vectors has attracted more and more attention in recent years. A key issue with bacteria-based delivery systems is how to regulate multiple protein drugs. Based on genetic code expansion technology, we developed a new strategy of using ncAAs as small molecular inducers for in situ protein regulation and engineered λ phage lysogen into a bacteria-based delivery system that can function in two delivery modes. Furthermore, this strategy enables independent regulation of multiple proteins by different ncAAs, offering important implications for combination therapy. This approach requires minimal genetic engineering efforts, and similar strategies can be applied to engineer other prophage-bacteria systems or study phage biology. This work expands the therapeutic applications of ncAAs and lysogenic phages.

Expanding the genetic code: In vivo approaches for incorporating non-proteinogenic monomers

The application of genetic code expansion has enabled the incorporation of non-canonical amino acids (ncAAs) into proteins, introducing novel functional groups and significantly broadening the scope of protein engineering. Over the past decade, this approach has extended beyond ncAAs to include non-proteinogenic monomers (npMs), such as β-amino acids and hydroxy acids. In vivo incorporation of these monomers requires maintaining orthogonality between endogenous and engineered aminoacyl-tRNA synthetase (aaRS)/tRNA pairs while optimizing the use of the translational machinery. This review introduces the fundamental principles of genetic code expansion and highlights the development of orthogonal aaRS/tRNA pairs and ribosomal engineering to incorporate npMs. Despite these advancements, challenges remain in engineering aaRS/tRNA pairs to accommodate npMs, especially monomers that differ significantly from L-α-amino acids due to their incompatibility with existing translational machinery. This review also introduces recent methodologies that allow aaRSs to recognize and aminoacylate npMs without reliance on the ribosomal translation system, thereby unlocking new possibilities for synthesizing biopolymers with chemically diverse monomers.

Optogenetics with Atomic Precision─A Comprehensive Review of Optical Control of Protein Function through Genetic Code Expansion

Conditional control of protein activity is important in order to elucidate the particular functions and interactions of proteins, their regulators, and their substrates, as well as their impact on the behavior of a cell or organism. Optical control provides a perhaps optimal means of introducing spatiotemporal control over protein function as it allows for tunable, rapid, and noninvasive activation of protein activity in its native environment. One method of introducing optical control over protein activity is through the introduction of photocaged and photoswitchable noncanonical amino acids (ncAAs) through genetic code expansion in cells and animals. Genetic incorporation of photoactive ncAAs at key residues in a protein provides a tool for optical activation, or sometimes deactivation, of protein activity. Importantly, the incorporation site can typically be rationally selected based on structural, mechanistic, or computational information. In this review, we comprehensively summarize the applications of photocaged lysine, tyrosine, cysteine, serine, histidine, glutamate, and aspartate derivatives, as well as photoswitchable phenylalanine analogues. The extensive and diverse list of proteins that have been placed under optical control demonstrates the broad applicability of this methodology.

Strategies to Expand the Genetic Code of Mammalian Cells

Genetic code expansion (GCE) in mammalian cells has emerged as a powerful technology for investigating and engineering protein function. This method allows for the precise incorporation of a rapidly growing toolbox of noncanonical amino acids (ncAAs) into predefined sites of target proteins expressed in living cells. Due to the minimal size of these genetically encoded ncAAs, the wide range of functionalities they provide, and the ability to introduce them freely at virtually any site of any protein by simple mutagenesis, this technology holds immense potential for probing the complex biology of mammalian cells and engineering next-generation biotherapeutics. In this review, we provide an overview of the underlying machinery that enables ncAA mutagenesis in mammalian cells and how these are developed. We have also compiled an updated list of ncAAs that have been successfully incorporated into proteins in mammalian cells. Finally, we provide our perspectives on the current challenges that need to be addressed to fully harness the potential of this technology.

Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design

Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes revealed critical contributions from second-shell - and even more distant - residues to their remarkable efficiency. In particular, such residues organize the internal electrostatic field to promote the reaction. Engineering such fields computationally proved to be a promising strategy, which, however, has some limitations. Charged residues necessarily form specific patterns of local interactions that may be exploited for structural integrity. As a result, it is impossible to probe the electrostatic field alone by substituting amino acids. We hypothesize that an approach that isolates the influences of residues' charges from other influences could yield deeper insights. We use molecular modeling with AI-enhanced QM/MM reaction sampling to implement such an approach and apply it to a model serine protease subtilisin. We find that the negative charge 8 Å away from the catalytic site is crucial to achieving the enzyme's catalytic efficiency, contributing more than 2 kcal/mol to lowering the barrier. In contrast, a positive charge from the second-closest charged residue opposes the efficiency of the reaction by raising the barrier by 0.8 kcal/mol. This result invites discussion into the role of this residue and trade-offs that might have taken place in the evolution of such enzymes. Our approach is transferable and can help investigate the evolution of electrostatic preorganization in other enzymes. We believe that the study and engineering of electrostatic fields in enzymes is a promising direction to advance both fundamental and applied enzymology and lead to the design of new powerful biocatalysts.

GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

Genome foundation models hold transformative potential for precision medicine, drug discovery, and understanding complex biological systems. However, existing models are often inefficient, constrained by suboptimal tokenization and architectural design, and biased toward reference genomes, limiting their representation of low-abundance, uncultured microbes in the rare biosphere. To address these challenges, we developed GenomeOcean, a 4-billion-parameter generative genome foundation model trained on over 600 Gbp of high-quality contigs derived from 220 TB of metagenomic datasets collected from diverse habitats across Earth's ecosystems. A key innovation of GenomeOcean is training directly on large-scale co-assemblies of metagenomic samples, enabling enhanced representation of rare microbial species and improving generalizability beyond genome-centric approaches. We implemented a byte-pair encoding (BPE) tokenization strategy for genome sequence generation, alongside architectural optimizations, achieving up to 150× faster sequence generation while maintaining high biological fidelity. GenomeOcean excels in representing microbial species and generating protein-coding genes constrained by evolutionary principles. Additionally, its fine-tuned model demonstrates the ability to discover novel biosynthetic gene clusters (BGCs) in natural genomes and perform zero-shot synthesis of biochemically plausible, complete BGCs. GenomeOcean sets a new benchmark for metagenomic research, natural product discovery, and synthetic biology, offering a robust foundation for advancing these fields.

Non-enzymatic posttranslational protein modifications in protein aggregation and neurodegenerative diseases

Highly reactive metabolic intermediates and other small molecules frequently react with amino acid side chains, leading to non-enzymatic posttranslational modifications (nPTMs) of proteins. The abundance of these modifications increases under high metabolic activity or stress conditions and can dramatically impact protein structure and function. Although protein quality control mechanisms typically mitigate the effects of these impaired proteins, in long-lived and degradation-resistant proteins, nPTMs accumulate. In some cases, such as cataract development and diabetes, clear links between nPTMs, aging, and disease progression have been established. In neurodegenerative diseases such as Alzheimer's and Parkinson's disease, a key question is whether accumulation of nPTMs is a cause or consequence of protein aggregation. This review focuses on major nPTMs found on proteins with central roles in neurodegenerative diseases such as α-synuclein, β-amyloid, and tau. We summarize current knowledge on the formation of these modifications and discuss their potential impact on disease onset and progression. Additionally, we examine what is known to date about how nPTMs impair cellular detoxification, repair, and degradation systems. Finally, we critically discuss the available methodologies to systematically investigate nPTMs at the molecular level and outline suitable approaches to study their effects on protein aggregation. We aim to foster more research into the role of nPTMs in neurodegeneration by adapting methodologies that have proven successful in studying enzymatic posttranslational modifications. Specifically, we advocate for site-specific incorporation of these modifications into target proteins using advanced chemical and molecular biology techniques.

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.

One-Step Maleimide-Based Dual Functionalization of Protein N-Termini

Maleimide derivatives are privileged reagents for chemically modifying proteins through the Michael addition reaction with cysteine due to their selectivity, operational simplicity, and commercial availability. However, since accessible free cysteine is rarely found in natural proteins, it is highly desirable to find alternative targets to enable direct bioconjugation of proteins with maleimides. In this study, we have developed an operationally simple and straightforward method for the N-terminal modification of proteins without the need for mutagenesis via a copper(II)-mediated [3+2] cycloaddition reaction with maleimides and 2-pyridinecarboxaldehyde (2-PCA) derivatives under non-denaturing conditions at pH 6 and 37 °C in aqueous media. Our method utilizes commercially available maleimides to attach diverse functionalities to various N-terminal amino acids. We demonstrate the preparation of a ternary protein complex cross-linked at the N-termini and dually modified trastuzumab equipped with monomethyl auristatin E (MMAE), a cytotoxic agent, and a Cy5 fluorophore (MMAE-Cy5-trastuzumab). MMAE-Cy5-trastuzumab retained human epidermal growth factor receptor 2 (HER2) recognition activity and exerted cytotoxicity against HER2-positive cells. Furthermore, MMAE-Cy5-trastuzumab allowed successful visualization of HER2-positive cancer cells in mouse tumors. This straightforward method will expand the accessibility of protein conjugates with well-defined structures in a wide range of research fields.

Genetic Code Expansion of the Silkworm Bombyx mori Using a Pyrrolysyl-tRNA Synthetase/tRNAPyl Pair

The domesticated silkworm Bombyx mori, an essential industrial animal for silk production, has attracted attention as a host for protein production due to its remarkable protein synthesis capability. Here, we applied genetic code expansion (GCE) using a versatile pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pair from Methanosarcina mazei to B. mori; GCE enables synthetic amino acid incorporation into proteins to give them non-natural functions. Transgenic B. mori lines expressing M. mazei PylRS and its cognate tRNAPyl were generated and cross-mated to obtain their F1 hybrid. Orally administering a click-compatible synthetic amino acid, trans-cyclooctene-lysine (TCO-Lys), to the F1 hybrid has led to the production of silk fiber incorporated with TCO-Lys. TCO-Lys incorporation in silk fiber was verified by selective labeling of the TCO group by click chemistry. The developed system is available for large-scale protein production with a wide variety of synthetic amino acids.

Genetically Recoding Respiratory Syncytial Virus to Visualize Nucleoprotein Dynamics and Virion Assembly

RNA viruses possess small genomes encoding a limited repertoire of essential and often multifunctional proteins. Although genetically tagging viral proteins provides a powerful tool for dissecting mechanisms of viral replication and infection, it remains a challenge. Here, we leverage genetic code expansion to develop a recoded strain of respiratory syncytial virus (RSV) in which the multifunctional nucleoprotein is site-specifically modified with a noncanonical amino acid. The resulting virus replicates exclusively in cells capable of amber stop codon suppression and is amenable to labeling with tetrazine-modified fluorophores, achieving high signal to background. Virus with labeled nucleoprotein remains functional, retaining ∼70% infectivity relative to unlabeled controls. We leverage this tool to visualize RSV assembly, capturing the transfer of nucleoprotein complexes from cytoplasmic condensates directly to budding viral filaments at the cell surface and to cytoplasmic compartments containing viral surface proteins. Collectively, these results suggest multiple pathways for RSV assembly and establish a framework that may be extended to other viral nucleoproteins.

Predicting the polyspecificity of aminoacyl-tRNA synthetase for non-canonical amino acids using molecular dynamics simulation and MM/PBSA

With the advancement of genetic code expansion, the field is progressing towards incorporating multiple non-canonical amino acids (ncAAs). The specificity of aminoacyl-tRNA synthetases (aaRSs) towards ncAAs is a critical factor, as engineered aaRSs frequently show polyspecificity, complicating the precise incorporation of multiple ncAAs. To address this challenge, predicting binding affinity can be beneficial. In this study, we expressed sfGFP using an orthogonal aaRS/tRNA pair with 4-Azido-L-phenylalanine (AzF) and another four different ncAAs. The experimental results showed specificity with O-Methyl-L-tyrosine as well as AzF, and these results were compared with computational predictions. We constructed a mutant aaRS structure specific for AzF through homology modelling and conducted docking studies with tyrosine and five ncAAs, followed by molecular dynamics simulations. The binding affinity was calculated using the molecular mechanics/Poisson-Boltzmann surface area, focusing on nonpolar solvation terms. While the analysis is based on the incorporation of limited number of ncAAs, the cavity and dispersion term method showed consistency with experimental data, highlighting its potential utility compared to the surface area term method. These findings enhance understanding of the ncAA specificity of aaRS in relation to computer simulations and energy calculations, which can be utilized to rationally design or predict the specificity of aaRS.

Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities

tRNAs are essential molecules in protein synthesis, responsible for translating the four-nucleotide genetic code into the corresponding amino acid sequence. RNA modifications play a crucial role in influencing tRNA folding, structure, and function. These modifications, ranging from simple methylations to complex hypermodified species, are distributed throughout the tRNA molecule. Depending on their type and position, they contribute to the accuracy and efficiency of decoding by participating in a complex network of interactions. The enzymatic processes introducing these modifications are equally intricate and diverse, adding further complexity. As a result, studying tRNA modifications faces limitations at multiple levels. This review addresses the challenges involved in manipulating and studying the function of tRNA modifications and discusses experimental strategies and possibilities to overcome these obstacles.

Beyond DAD: proposing a one-letter code for nucleobase-mediated molecular recognition

Nucleobase binding is a fundamental molecular recognition event central to modern biological and bioinspired supramolecular research. Underpinning this recognition is a deceptively simple hydrogen-bonding code, primarily based on the canonical nucleobases in DNA and RNA. Inspired by these biotic structures, chemists and biologists have designed abiotic hydrogen-bonding motifs that can interact with, augment, and reshape native molecular recognition, for applications ranging from genetic code expansion and nucleic acid recognition to supramolecular materials utilizing mono- and bifacial nucleobases. However, as the number of nucleobase-inspired motifs expands, the absence of a standard vocabulary to describe hydrogen bond (HB) patterns has led to a haphazard mixture of shorthand descriptors that are confusing and inconsistent. Alternative notations that specify individual HB sites (such as DAD for donor-acceptor-donor) are cumbersome for biological and supramolecular constructs that contain many such patterns. This situation creates a barrier to sharing and interpreting nucleobase-related research across sub-disciplines, hindering collaboration and innovation. In this perspective, we aim to initiate discourse on this issue by considering what would be needed to formulate a concise one-letter code for the HB patterns associated with synthetic nucleobases. We first summarize some of the issues caused by the current absence of a consistent naming scheme. Subsequently, we discuss some key considerations in designing a coherent naming system. Finally, we leverage chemical rationale and pedagogical mnemonic considerations to propose a succinct and intuitive one-letter code for supramolecular two- and three-HB motifs. We hope that this discussion will spark conversations within our interdisciplinary community, thereby facilitating collaboration and easing communication among researchers engaged in synthetic nucleobase design.

GPCR Biosensors to Study Conformational Dynamics and Signaling in Drug Discovery

G protein-coupled receptors (GPCRs) are a superfamily of transmembrane signal transducers that facilitate the flow of chemical signals across membranes. GPCRs are a desirable class of drug targets, and the activation and deactivation dynamics of these receptors are widely studied. Multidisciplinary approaches for studying GPCRs, such as downstream biochemical signaling assays, cryo-electron microscopy structural determinations, and molecular dynamics simulations, have provided insights concerning conformational dynamics and signaling mechanisms. However, new approaches including biosensors that use luminescence- and fluorescence-based readouts have been developed to investigate GPCR-related protein interactions and dynamics directly in cellular environments. Luminescence- and fluorescence-based readout approaches have also included the development of GPCR biosensor platforms that utilize enabling technologies to facilitate multiplexing and miniaturization. General principles underlying the biosensor platforms and technologies include scalability, orthogonality, and kinetic resolution. Further application and development of GPCR biosensors could facilitate hit identification in drug discovery campaigns. The goals of this review are to summarize developments in the field of GPCR-related biosensors and to discuss the current available technologies.

Creating a System of Dual Regulation of Translation and Transcription to Enhance the Production of Recombinant Protein

When constructing cell factories, it is crucial to reallocate intracellular resources towards the synthesis of target compounds. However, imbalanced resource allocation can lead to a tradeoff between cell growth and production, reducing overall efficiency. Reliable gene expression regulation tools are needed to coordinate cell growth and production effectively. The orthogonal translation system, developed based on genetic code expansion (GCE), incorporates non-canonical amino acids (ncAAs) into proteins by assigning them to expanded codons, which enables the control of target protein expression at the translational level in an ncAA-dependent manner. However, the stringency of this regulatory tool remains inadequate. This study achieved strict translational-level control of the orthogonal translation system by addressing the abnormal leakage caused by the arabinose-inducible promoter. Further validation was conducted on the relationship between ncAA concentration and expression level, as well as the host's adaptability to the system. Subsequently, the system's applicability across multiple Escherichia coli hosts was verified by examining the roles of RF1 (peptide chain release factor 1) and endogenous TAG codons. By combining this strategy with inducible promoters, dual-level regulation of target gene expression at both transcriptional and translational levels was achieved and the dynamic range was further increased to over 20-fold. When using ncAA to control the expression of T7 RNA polymerase (T7 RNAP), the leakage expression was reduced by 82.7%, mitigating the low production efficiency caused by extensive leakage in the T7 system. As proof of concept, the strategy enhanced the production of alcohol dehydrogenase (ADH) by 9.82-fold, demonstrating its excellent capability in controlling gene expression in developing cell factories.

Noncanonical Amino Acid Tools and Their Application to Membrane Protein Studies

Methods rooted in chemical biology have contributed significantly to studies of integral membrane proteins. One recent key approach has been the application of genetic code expansion (GCE), which enables the site-specific incorporation of noncanonical amino acids (ncAAs) with defined chemical properties into proteins. Efficient GCE is challenging, especially for membrane proteins, which have specialized biogenesis and cell trafficking machinery and tend to be expressed at low levels in cell membranes. Many eukaryotic membrane proteins cannot be expressed functionally in E. coli and are most effectively studied in mammalian cell culture systems. Recent advances have facilitated broader applications of GCE for studies of membrane proteins. First, AARS/tRNA pairs have been engineered to function efficiently in mammalian cells. Second, bioorthogonal chemical reactions, including cell-friendly copper-free "click" chemistry, have enabled linkage of small-molecule probes such as fluorophores to membrane proteins in live cells. Finally, in concert with advances in GCE methodology, the variety of available ncAAs has increased dramatically, thus enabling the investigation of protein structure and dynamics by multidisciplinary biochemical and biophysical approaches. These developments are reviewed in the historical framework of the development of GCE technology with a focus on applications to studies of membrane proteins.

Installation of an organocatalyst into a protein scaffold creates an artificial Stetterase

Using a protein scaffold covalently functionalised with a thiamine-inspired N-heterocyclic carbene (NHC), we created an artificial Stetterase (ArtiSt) which catalyses a stereoselective, intramolecular Stetter reaction. We demonstrate that ArtiSt functions under ambient conditions with low catalyst loading. Furthermore, activity can be increased >20 fold by altering the protein scaffold.

Genetic Code Expansion History and Modern Innovations

The genetic code is the foundation for all life. With few exceptions, the translation of nucleic acid messages into proteins follows conserved rules, which are defined by codons that specify each of the 20 proteinogenic amino acids. For decades, leading research groups have developed a catalogue of innovative approaches to extend nature's amino acid repertoire to include one or more noncanonical building blocks in a single protein. In this review, we summarize advances in the history of in vitro and in vivo genetic code expansion, and highlight recent innovations that increase the scope of biochemically accessible monomers and codons. We further summarize state-of-the-art knowledge in engineered cellular translation, as well as alterations to regulatory mechanisms that improve overall genetic code expansion. Finally, we distill existing limitations of these technologies into must-have improvements for the next generation of technologies, and speculate on future strategies that may be capable of overcoming current gaps in knowledge.

Reaching New Heights in Genetic Code Manipulation with High Throughput Screening

The chemical and physical properties of proteins are limited by the 20 canonical amino acids. Genetic code manipulation allows for the incorporation of noncanonical amino acids (ncAAs) that enhance or alter protein functionality. This review explores advances in the three main strategies for introducing ncAAs into biosynthesized proteins, focusing on the role of high throughput screening in these advancements. The first section discusses engineering aminoacyl-tRNA synthetases (aaRSs) and tRNAs, emphasizing how novel selection methods improve characteristics including ncAA incorporation efficiency and selectivity. The second section examines high-throughput techniques for improving protein translation machinery, enabling accommodation of alternative genetic codes. This includes opportunities to enhance ncAA incorporation through engineering cellular components unrelated to translation. The final section highlights various discovery platforms for high-throughput screening of ncAA-containing proteins, showcasing innovative binding ligands and enzymes that are challenging to create with only canonical amino acids. These advances have led to promising drug leads and biocatalysts. Overall, the ability to discover unexpected functionalities through high-throughput methods significantly influences ncAA incorporation and its applications. Future innovations in experimental techniques, along with advancements in computational protein design and machine learning, are poised to further elevate this field.

Tuning the Functionality of Designer Translating Organelles with Orthogonal tRNA Synthetase/tRNA Pairs

Site-specific incorporation of noncanonical amino acids (ncAAs) can be realized by genetic code expansion (GCE) technology. Different orthogonal tRNA synthetase/tRNA (RS/tRNA) pairs have been developed to introduce a ncAA at the desired site, delivering a wide variety of functionalities that can be installed into selected proteins. Cytoplasmic expression of RS/tRNA pairs can cause a problem with background ncAA incorporation into host proteins. The application of orthogonally translating organelles (OTOs), inspired by the concept of phase separation, provides a solution for this issue in mammalian cells, allowing site-specific and protein-selective ncAA incorporation. So far, only Methanosarcina mazei (Mm) pyrrolysyl-tRNA synthetase (PylRS) has been used within OTOs, limiting the method's potential. Here, we explored the implementation of four other widely used orthogonal RS/tRNA pairs with OTOs, which, to our surprise, were unsuccessful in generating mRNA-selective GCE. Next, we tested several experimental solutions and developed a new chimeric phenylalanyl-RS/tRNA pair that enables ncAA incorporation in OTOs in a site-specific and protein-selective manner. Our work reveals unaccounted design constraints in the spatial engineering of enzyme functions using designer organelles and presents a strategy to overcome those in vivo. We then discuss current limitations and future directions of in-cell engineering in general and protein engineering using GCE specifically.

Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis

Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.

Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis

This review aims to provide an overview of the progress in protein-based artificial photosystem design and their potential to uncover the underlying principles governing light-harvesting in photosynthesis. While significant advances have been made in this area, a gap persists in reviewing these advances. This review provides a perspective of the field, pinpointing knowledge gaps and unresolved challenges that warrant further inquiry. In particular, it delves into the key considerations when designing photosystems based on the chromophore and protein scaffold characteristics, presents the established strategies for artificial photosystems engineering with their advantages and disadvantages, and underscores the recent breakthroughs in understanding the molecular mechanisms governing light-harvesting, charge separation, and the role of the protein motions in the chromophore's excited state relaxation. By disseminating this knowledge, this article provides a foundational resource for defining the field of bio-hybrid photosystems and aims to inspire the continued exploration of artificial photosystems using protein design.

An expanded molecular and systems toolbox for imaging, mapping, and controlling local translation

Localized protein translation occurs through trafficking of mRNAs and protein translation machineries to different compartments of the cell, leading to rapid on-site synthesis of proteins in response to signaling cues. The spatiotemporally precise nature of the local translation process necessitates continual developments of technologies reviewed herein to visualize and map biomolecular components and the translation process with better spatial and temporal resolution and with fewer artifacts. We also discuss approaches to control local translation, which can serve as a design paradigm for subcellular genetic devices for eukaryotic synthetic biology.

Engineering of Recombinant Human Papillomavirus 16 L1 Protein for Incorporation with para-Azido-L-Phenylalanine

Human papillomavirus (HPV) L1 capsid protein were produced in several host systems, but few studies have focused on enhancing the properties of the L1 protein. In this study, we aimed to produce recombinant Human papillomavirus (HPV) L1 capsid protein containing para-azido-L-phenylalanine (pAzF) in Escherichia coli. First, we expressed the maltose-binding protein (MBP)-fused HPV16 L1, and 5 residues in HPV16 L1 protein were selected by the in silico modeling for amber codon substitution. Among the variants of the five locations, we identified a candidate that exhibited significant differences in expression with and without pAzF via genetic code expansion (GCE). The expressed recombinant MBP-HPV16L1 protein was confirmed for incorporation of pAzF and the formation of VLPs was tested in vitro.

Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation

Genetic code expansion (GCE) has become a critical tool in biology by enabling the site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Central to GCE is the development of orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs wherein engineered aaRSs recognize chosen ncAAs and charge them onto tRNAs that decode blank codons ( e.g ., the amber stop codon). Many orthogonal aaRS/tRNA pairs covering a wide range of ncAAs have been generated by directed evolution, yet the evolution of new aaRS/tRNA pairs by standard strategies remains a labor-intensive process that often produces aaRS/tRNA pairs with suboptimal ncAA incorporation efficiencies. In this study, we present a strategy for evolving aaRSs that leverages OrthoRep to drive their continuous hypermutation in yeast. We demonstrate our strategy in 8 independent aaRS evolution campaigns starting from 4 different aaRS/tRNA parents targeting 7 distinct ncAAs. We observed the rapid evolution of multiple novel aaRSs capable of incorporating an overall range of 13 ncAAs tested into proteins in response to the amber codon. Some evolved systems reached efficiencies for amber codon-specified ncAA-dependent translation comparable to translation with natural amino acids specified by sense codons in yeast. Additionally, we discovered a surprising aaRS that evolved to self-regulate its own expression for greater dependency on ncAAs for translation. These findings demonstrate the potential of OrthoRep-driven aaRS evolution platforms in supporting the continued growth of GCE technologies.

Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology

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.

Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion

Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.

Chemical Synthesis of Human Proteoforms and Application in Biomedicine

Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.

Bioproduction Platform to Generate Functionalized Disulfide-Constrained Peptide Analogues

Disulfide-constrained peptides (DCPs) have gained increased attention as a drug modality due to their exceptional stability and combined advantages of large biologics and small molecules. Chemical synthesis, although widely used to produce DCPs, is associated with high cost, both economically and environmentally. To reduce the dependence on solid phase peptide synthesis and the negative environmental footprint associated with it, we present a highly versatile, low-cost, and environmentally friendly bioproduction platform to generate DCPs and their conjugates as well as chemically modified or isotope-labeled DCPs. Using the DCP against the E3 ubiquitin ligase Zinc and Ring Finger 3, MK1-3.6.10, as a model peptide, we have demonstrated the use of bacterial expression, combined with Ser ligation or transglutaminase-mediated XTEN ligation, to produce multivalent MK1-3.6.10 and MK1-3.6.10 with N-terminal functional groups. We have also developed a bioproduction method for the site-specific incorporation of unnatural amino acids into recombinant DCPs by the amber codon suppression system. Lastly, we produced 15N/13C-labeled MK1-3.6.10 with high yield and assessed the performance of a semiautomated resonance assignment workflow that could be used to accelerate binding studies and structural characterization of DCPs. This study provides a proof of concept to generate functionalized DCPs using bioproduction, providing a potential solution to alleviate the reliance on hazardous chemicals, reduce the cost, and expedite the timeline for DCP discovery.

Designing a Novel Temperature- and Noncanonical Amino Acid-Controlled Biological Logic Gate in Escherichia coli

Genetic code expansion (GCE) is a powerful strategy that expands the genetic code of an organism for incorporating noncanonical amino acids into proteins using engineered tRNAs and aminoacyl-tRNA synthetases (aaRSs). While GCE has opened up new possibilities for synthetic biology, little is known about the potential side effects of exogenous aaRS/tRNA pairs. In this study, we investigated the impact of exogenous aaRS and amber suppressor tRNA on gene expression in Escherichia coli. We discovered that in DH10β ΔcyaA, transformed with the F1RP/F2P two-hybrid system, the high consumption rate of cellular adenosine triphosphate by exogenous aaRS/tRNA at elevated temperatures induces temperature sensitivity in the expression of genes regulated by the cyclic AMP receptor protein (CRP). We harnessed this temperature sensitivity to create a novel biological AND gate in E. coli, responsive to both p-benzoylphenylalanine (BzF) and low temperature, using a BzF-dependent variant of E. coli chorismate mutase and split subunits of Bordetella pertussis adenylate cyclase. Our study provides new insights into the unexpected effects of exogenous aaRS/tRNA pairs and offers a new approach for constructing a biological logic gate.

Site-Specific Antibody Prodrugs via S-Arylation: a Bioconjugation Approach Toward Masked Tyrosine Analogues

The utility of antibody therapeutics is hampered by potential cross-reactivity with healthy tissue. Over the past decade, significant advances have been made in the design of activatable antibodies, which increase, or create altogether, the therapeutic window of a parent antibody. Of these, antibody prodrugs (pro-antibodies) are masked antibodies that have advanced the most for therapeutic use. They are designed to reveal the active, parent antibody only when encountering proteases upregulated in the microenvironment of the targeted disease tissue, thereby minimizing off-target activity. However, current pro-antibody designs are relegated to fusion proteins that append masking groups restricted to the use of only canonical amino acids, offering excellent control of the site of introduction, but with no authority over where the masking group is installed other than the N-terminus of the antibody. Here, we present a palladium-based bioconjugation approach for the site-specific introduction of a masked tyrosine mimic in the complementary determining region of the FDA approved antibody therapeutic ipilimumab used as a model system. The approach enables the introduction of a protease cleavable group tethered to noncanonical polymers (polyethylene glycol (PEG)) resulting in 47-fold weaker binding to cells expressing CTLA-4, the target antigen of ipilimumab. Upon exposure to tumor-associated proteases, the masking group is cleaved, unveiling a tyrosine-mimic (dubbed hydroxyphenyl cysteine (HPC)) that restores (>90% restoration) binding affinity to its target antigen.

A tRNA modification pattern that facilitates interpretation of the genetic code

Interpretation of the genetic code from triplets of nucleotides to amino acids is fundamental to life. This interpretation is achieved by cellular tRNAs, each reading a triplet codon through its complementary anticodon (positions 34-36) while delivering the amino acid charged to its 3'-end. This amino acid is then incorporated into the growing polypeptide chain during protein synthesis on the ribosome. The quality and versatility of the interpretation is ensured not only by the codon-anticodon pairing, but also by the post-transcriptional modifications at positions 34 and 37 of each tRNA, corresponding to the wobble nucleotide at the first position of the anticodon and the nucleotide on the 3'-side of the anticodon, respectively. How each codon is read by the matching anticodon, and which modifications are required, cannot be readily predicted from the codon-anticodon pairing alone. Here we provide an easily accessible modification pattern that is integrated into the genetic code table. We focus on the Gram-negative bacterium Escherichia coli as a model, which is one of the few organisms whose entire set of tRNA modifications and modification genes is identified and mapped. This work provides an important reference tool that will facilitate research in protein synthesis, which is at the core of the cellular life.

Reading and Writing the Ubiquitin Code Using Genetic Code Expansion

Deciphering ubiquitin proteoform signaling and its role in disease has been a long-standing challenge in the field. The effects of ubiquitin modifications, its relation to ubiquitin-related machineries, and its signaling output has been particularly limited by its reconstitution and means of characterization. Advances in genetic code expansion have contributed towards addressing these challenges by precision incorporation of unnatural amino acids through site selective codon suppression. This review discusses recent advances in studying the 'writers', 'readers', and 'erasers' of the ubiquitin code using genetic code expansion. Highlighting strategies towards genetically encoded protein ubiquitination, ubiquitin phosphorylation, acylation, and finally surveying ubiquitin interactions, we strive to bring attention to this unique approach towards addressing a widespread proteoform problem.

Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers

Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Insights into the dynamics of the Ca2+ release-activated Ca2+ channel pore-forming complex Orai1

An important calcium (Ca2+) entry pathway into the cell is the Ca2+ release-activated Ca2+ (CRAC) channel, which controls a series of downstream signaling events such as gene transcription, secretion and proliferation. It is composed of a Ca2+ sensor in the endoplasmic reticulum (ER), the stromal interaction molecule (STIM), and the Ca2+ ion channel Orai in the plasma membrane (PM). Their activation is initiated by receptor-ligand binding at the PM, which triggers a signaling cascade within the cell that ultimately causes store depletion. The decrease in ER-luminal Ca2+ is sensed by STIM1, which undergoes structural rearrangements that lead to coupling with Orai1 and its activation. In this review, we highlight the current understanding of the Orai1 pore opening mechanism. In this context, we also point out the questions that remain unanswered and how these can be addressed by the currently emerging genetic code expansion (GCE) technology. GCE enables the incorporation of non-canonical amino acids with novel properties, such as light-sensitivity, and has the potential to provide novel insights into the structure/function relationship of CRAC channels at a single amino acid level in the living cell.

Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid

The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.

Cell-selective bioorthogonal labeling

In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.

Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging

Structural dynamics of human immunodeficiency virus 1 (HIV-1) envelope (Env) glycoprotein mediate cell entry and facilitate immune evasion. Single-molecule FRET using peptides for Env labeling revealed structural dynamics of Env, but peptide use risks potential effects on structural integrity/dynamics. While incorporating noncanonical amino acids (ncAAs) into Env by amber stop-codon suppression, followed by click chemistry, offers a minimally invasive approach, this has proved to be technically challenging for HIV-1. Here, we develope an intact amber-free HIV-1 system that overcomes hurdles of preexisting viral amber codons. We achieved dual-ncAA incorporation into Env on amber-free virions, enabling single-molecule Förster resonance energy transfer (smFRET) studies of click-labeled Env that validated the previous peptide-based labeling approaches by confirming the intrinsic propensity of Env to dynamically sample multiple conformational states. Amber-free click-labeled Env also enabled real-time tracking of single virion internalization and trafficking in cells. Our system thus permits in-virus bioorthogonal labeling of proteins, compatible with studies of virus entry, trafficking, and egress from cells.

Selenium chemistry for spatio-selective peptide and protein functionalization

The ability to construct a peptide or protein in a spatio-specific manner is of great interest for therapeutic and biochemical research. However, the various functional groups present in peptide sequences and the need to perform chemistry under mild and aqueous conditions make selective protein functionalization one of the greatest synthetic challenges. The fascinating paradox of selenium (Se) - being found in both toxic compounds and also harnessed by nature for essential biochemical processes - has inspired the recent exploration of selenium chemistry for site-selective functionalization of peptides and proteins. In this Review, we discuss such approaches, including metal-free and metal-catalysed transformations, as well as traceless chemical modifications. We report their advantages, limitations and applications, as well as future research avenues.

Expanding the Genetic Code of Xenopus laevis Embryos

The incorporation of unnatural amino acids into proteins through genetic code expansion has been successfully adapted to African claw-toed frog embryos. Six unique unnatural amino acids are incorporated site-specifically into proteins and demonstrate robust and reliable protein expression. Of these amino acids, several are caged analogues that can be used to establish conditional control over enzymatic activity. Using light or small molecule triggers, we exhibit activation and tunability of protein functions in live embryos. This approach was then applied to optical control over the activity of a RASopathy mutant of NRAS, taking advantage of generating explant cultures from Xenopus. Taken together, genetic code expansion is a robust approach in the Xenopus model to incorporate novel chemical functionalities into proteins of interest to study their function and role in a complex biological setting.

Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains

Neurotransmitter receptors are essential components of synapses for communication between neurons in the brain. Because the spatiotemporal expression profiles and dynamics of neurotransmitter receptors involved in many functions are delicately governed in the brain, in vivo research tools with high spatiotemporal resolution for receptors in intact brains are highly desirable. Covalent labeling by chemical reaction (chemical labeling) of proteins without genetic manipulation is now a powerful method for analyzing receptors in vitro. However, selective target receptor labeling in the brain has not yet been achieved. This study shows that ligand-directed alkoxyacylimidazole (LDAI) chemistry can be used to selectively tether synthetic probes to target endogenous receptors in living mouse brains. The reactive LDAI reagents with negative charges were found to diffuse well over the whole brain and could selectively label target endogenous receptors, including AMPAR, NMDAR, mGlu1, and GABAAR. This simple and robust labeling protocol was then used for various applications: three-dimensional spatial mapping of endogenous receptors in the brains of healthy and disease-model mice; multi-color receptor imaging; and pulse-chase analysis of the receptor dynamics in postnatal mouse brains. Here, results demonstrated that bioorthogonal receptor modification in living animal brains may provide innovative molecular tools that contribute to the in-depth understanding of complicated brain functions.