Red and far-red cleavable fluorescent dyes for self-labelling enzyme protein tagging and interrogation of GPCR co-internalization

Post-labelling cleavable substrates for self-labelling protein tags, such as SNAP- and Halo-tags, can be used to study cell surface receptor trafficking events by stripping dyes from non-internalized protein pools. Since the complexity of receptor biology requires the use of multiple and orthogonal approaches to simultaneously probe multiple receptor pools, we report the development of four membrane impermeable probes that covalently bind to either the SNAP- or the Halo-tag in the red to far-red range. These molecules bear a disulfide bond to release the non-internalized probe using the reducing agent sodium 2-mercaptoethane sulfonate (MESNA). As such, our approach allows the simultaneous visualization of multiple internalized cell surface proteins in two colors which we showcase using G protein-coupled receptors. We use this approach to detect internalized group II metabotropic glutamate receptor (mGluRs), homo- and heterodimers, and to reveal unidirectional crosstalk between co-expressed glucagon-like peptide 1 (GLP1R) and glucose-dependent insulinotropic polypeptide receptors (GIPR). In these applications, we translate our method to both high resolution imaging and quantitative, high throughput assays, demonstrating the value of our approach for a wide range of applications.

Identification of Low-Density Lipoprotein Receptor-Related Protein 1 as a CXCL14 Receptor Using Chemically Synthesized Tetrafunctional Probes

CXCL14 is a primordial CXC-type chemokine that transports CpG oligodeoxynucleotides (ODN) into endosomes and lysosomes in dendritic cells, thereby leading to the activation of the Toll-like receptor 9 (TLR9)-mediated innate immune system. However, the underlying molecular mechanism by which the CXCL14-CpG ODN complex enters cells remains elusive. Herein, we describe the chemical synthesis of CXCL14-derived photoaffinity probes and their application to the identification of target receptors for CXCL14 using quantitative proteomics. By utilizing native chemical ligation and maleimide-thiol coupling chemistry, we synthesized site-specifically modified CXCL14-based photoaffinity probes that contain photoreactive 2-aryl-5-carboxytetrazole (ACT) and a hydrazine-labile cleavable linker. CXCL14-based probes were found to be capable of binding CpG ODN to immune cells, whose bioactivities were comparable to native CXCL14. Application of CXCL14-derived probes to quantitative proteomic experiments enabled the identification of dozens of target receptor candidates for CXCL14 in mouse macrophage-derived RAW264.7 cells, and we discovered that low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for CXCL14 by competitive proteome profiling. We further showed that disruption of LRP1 affected the incorporation of the CXCL14-CpG ODN complex in the cells. Overall, this report highlights the power of synthetic CXCL14-derived photoaffinity probes combined with chemical proteomics to discover previously unidentified receptors for CXCL14, which could promote an understanding of the molecular functions of CXCL14 and the elaborate machinery of innate immune systems.

Copper-Catalyzed Azide-Alkyne Cycloaddition-Oriented Multifunctional Bio-Orthogonal Linker BPPA: Design, Synthesis and Evaluation

The multifunctional linker molecules are crucial for the bio-orthogonal reaction for proteomic target profiling. Herein, we wish to present a novel type of biotin-based tetra-functional bio-orthogonal linkers 3a-3h named BPPA which, possessing a unique photolabile phenacyl ester motif, were readily prepared in 85-90% yields by a simple and green one-step protocol from commercially available and inexpensive reagents of biotin acids and 4'-ethynyl/azido 2-bromoacetophenones. The typical click reaction of BPPA linkers 3a and 3e via copper-catalyzed azide-alkyne cycloaddition (CuAAC) took place easily, resulting in the corresponding BPPA-triazole adducts 4a and 4b in nearly quantitative yields. A further cleavability evaluation of 4a and 4b demonstrated that the expected C-O bond detachment could be accomplished efficiently and rapidly by UV irradiation or by ammonia hydrolysis, respectively, resulting in the residual (hydroxyl)acetylphenyl triazole fragment supposed to be attached to proteins during biological manipulations. The BPPA linkers, with dual clickable options of either the terminal azide or alkyne clickable group, exhibit high potentials for various CuAAC-oriented bio-orthogonal reactions.

Spatiotemporal Investigation of Intercellular Heterogeneity via Multiple Photocaged Probes

Intercellular heterogeneity occurs widely under both normal physiological environments and abnormal disease-causing conditions. Several attempts to couple spatiotemporal information to cell states in a microenvironment were performed to decipher the cause and effect of heterogeneity. Furthermore, spatiotemporal manipulation can be achieved with the use of photocaged/photoactivatable molecules. Here, we provide a platform to spatiotemporally analyze differential protein expression in neighboring cells by multiple photocaged probes coupled with homemade photomasks. We successfully established intercellular heterogeneity (photoactivable ROS trigger) and mapped the targets (directly ROS-affected cells) and bystanders (surrounding cells), which were further characterized by total proteomic and cysteinomic analysis. Different protein profiles were shown between bystanders and target cells in both total proteome and cysteinome. Our strategy should expand the toolkit of spatiotemporal mapping for elucidating intercellular heterogeneity.

Simple purification of small-molecule-labelled peptides via palladium enolate formation from β-ketoamide tags

Palladium enolates derived from β-ketocarbonyl compounds serve as key intermediates in various catalytic asymmetric reactions. We found that the palladium enolate formed from β-ketoamide is stable in air and moisture and we applied this property to develop a peptide purification system using β-ketoamide as a small affinity tag in aqueous media. A solid-supported palladium complex successfully captured β-ketoamide-tagged molecules as palladium enolates and released them in high yield upon acid treatment. Optimum conditions for the catch and release of tagged peptides from a mixture of untagged peptides were established. To demonstrate the value of this methodology in identifying the binding site of a ligand to its target protein, we purified and identified a peptide containing the ligand-binding site from the tryptic digest of cathepsin B labelled with a covalent cathepsin B inhibitor containing a β-ketoamide tag.

Mapping Peptide-Protein Interactions by Amine-Reactive Cleavable Photoaffinity Reagents

Photoaffinity labeling followed by tandem mass spectrometry is an often used strategy to identify protein targets of small-molecule drugs or drug candidates, which, under ideal conditions, enables the identification of the actual drug binding site. In the case of bioactive peptides, however, identifying the distinct binding site is hampered because of complex fragmentation patterns during tandem mass spectrometry. We here report the development and use of small cleavable photoaffinity reagents that allow functionalization of bioactive peptides for light-induced covalent binding to their protein targets. Upon cleavage of the covalently linked peptide drug, a chemical remnant of a defined mass remains on the bound amino acid, which is then used to unambiguously identify the drug binding site. Applying our approach to known peptide-drug/protein pairs with reported crystal structures, such as the calmodulin-melittin interaction, we were able to validate the identified binding sites based on structural models. Overall, our cleavable photoaffinity labeling strategy represents a powerful tool to enable the identification of protein targets and specific binding sites of a wide variety of bioactive peptides in the future.

Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes

New protein synthesis is regulated both at the level of mRNA transcription and translation. RNA-Seq is effective at measuring levels of mRNA expression, but techniques to monitor mRNA translation are much more limited. Previously, we reported results from O-propargyl-puromycin (OPP) labeling of proteins undergoing active translation in a 2-h time frame, followed by biotinylation using click chemistry, affinity purification, and on-bead digestion to identify nascent proteins by mass spectrometry (OPP-ID). As with any on-bead digestion protocol, the problem of nonspecific binders complicated the rigorous categorization of nascent proteins by OPP-ID. Here, we incorporate a chemically cleavable linker, Dde biotin-azide, into the protocol (OPP-ID_CL) to provide specific release of modified proteins from the streptavidin beads. Following capture, the Dde moiety is readily cleaved with 2% hydrazine, releasing nascent polypeptides bearing OPP plus a residual C₃H₈N₄ tag. When results are compared side by side with the original OPP-ID method, change to a cleavable linker led to a dramatic reduction in the number of background proteins detected in controls and a concomitant increase in the number of proteins that could be characterized as newly synthesized. We evaluated the method's ability to detect nascent proteins at various submilligram protein input levels and showed that, when starting with only 100 μg of protein, ∼1500 nascent proteins could be identified with low background. Upon treatment of K562 cells with MLN128, a potent inhibitor of the mammalian target of rapamycin, prior to OPP treatment, we identified 1915 nascent proteins, the majority of which were downregulated upon inhibitor treatment. Repressed proteins with log2 FC <-1 revealed a complex network of functionally interacting proteins, with the largest cluster associated with translational initiation. Overall, incorporation of the Dde biotin-azide cleavable linker into our protocol has increased the depth and accuracy of profiling of nascent protein networks.

Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics

Click chemistry─specifically the copper-catalyzed azide-alkyne cycloaddition─has enabled the development of a wide range of chemical probes to analyze subsets of the functional proteome. The "clickable" proteome can be selectively enriched by using diverse cleavable biotin tags, but the direct identification of probe/tag-modified peptides (or peptide-centric analysis) remains challenging. Here, we evaluated the performance of five commercially available cleavable biotin tags in three most common chemoproteomic workflows, resulting in a comparative analysis of 15 methods. An acid-cleavable biotin tag with a dialkoxydiphenylsilane moiety, in combination with the protein "click", peptide "capture" workflow, outperforms all other methods in terms of enrichment efficiency, identification yield, and reproducibility, although its performance may be slightly compromised by the formation of an unwanted formate product revealed by blind search. Despite being inferior, photocleavable, and reduction-cleavable, biotin tags can also find their applicable sceneries, especially when dealing with acid-sensitive probes or probe-derived modifications. Furthermore, the systematic comparison of LC-MS/MS characteristics of tag-modified peptides provides valuable information for the future development of cleavable biotin reagents. Taken together, our data provides a much-needed practical guidance for researchers interested in developing and/or applying an ideal cleavable biotin tag to peptide-centric chemoproteomics.

Protein Lipidation Types: Current Strategies for Enrichment and Characterization

Post-translational modifications regulate diverse activities of a colossal number of proteins. For example, various types of lipids can be covalently linked to proteins enzymatically or non-enzymatically. Protein lipidation is perhaps not as extensively studied as protein phosphorylation, ubiquitination, or glycosylation although it is no less significant than these modifications. Evidence suggests that proteins can be attached by at least seven types of lipids, including fatty acids, lipoic acids, isoprenoids, sterols, phospholipids, glycosylphosphatidylinositol anchors, and lipid-derived electrophiles. In this review, we summarize types of protein lipidation and methods used for their detection, with an emphasis on the conjugation of proteins with polyunsaturated fatty acids (PUFAs). We discuss possible reasons for the scarcity of reports on PUFA-modified proteins, limitations in current methodology, and potential approaches in detecting PUFA modifications.

Improved Handling of Peptide Segments Using Side Chain-Based "Helping Hand" Solubilizing Tools

Maintaining high, or even sufficient, solubility of every peptide segment in chemical protein synthesis (CPS) remains a critical challenge; insolubility of just a single peptide segment can thwart a total synthesis venture. Multiple approaches have been used to address this challenge, most commonly by employing a chemical tool to temporarily improve peptide solubility. In this chapter, we discuss chemical tools for introducing semipermanent solubilizing sequences (termed helping hands) at the side chains of Lys and Glu residues. We describe the synthesis, incorporation by Fmoc-SPPS, and cleavage conditions for utilizing these two tools. For Lys sites, we discuss the Fmoc-Ddap-OH dimedone-based linker, which is achiral, synthesized in one step, can be introduced directly at primary amines, and is removed using hydroxylamine (or hydrazine). For Glu sites, we detail the new Fmoc-SPPS building block, Fmoc-Glu(AlHx)-OH, which can be prepared in an efficient process over two purifications. Solubilizing sequences are introduced directly on-resin and later cleaved with palladium-catalyzed transfer under aqueous conditions to restore a native Glu side chain. These two chemical tools are straightforward to prepare and implement, and we anticipate continued usage in "difficult" peptide segments following the protocols described herein.

Automated High-Throughput Method for the Fast, Robust, and Reproducible Enrichment of Newly Synthesized Proteins

A high-throughput method was developed for the automated enrichment of newly synthesized proteins (NSPs), which are labeled metabolically by substituting methionine with the “click-able” analogue azidohomoalanine (AHA). A suitable conjugate containing a dibenzocyclooctyne (DBCO) group allows the specific selection of NSPs by a fast 1 h click chemistry-based reaction with AHA. Through an automated pipetting platform, the samples are loaded into streptavidin cartridges for the selective binding of the NSPs by means of a biotin bait contained in the conjugate. The enriched proteins are eluted by a reproducible chemical cleavage of the 4,4-dimethyl-2,6-dioxocyclohexylidene (Dde) group in the conjugate, which increases selectivity. The NSPs can be collected and digested in the same well plate, and the resulting peptides can be subsequently loaded for automated cleanup, followed by mass spectrometry analysis. The proposed automated method allows for the robust and effective enrichment of samples in 96-well plates in a period of 3 h. Our developed enrichment method was comprehensively evaluated and then applied to the proteomics analysis of the melanoma A375 cell secretome, after treatment with the cytokines interferon α (IFN-α) and γ (IFN-γ), resulting in the quantification of 283 and 263 proteins, respectively, revealing intricate tumor growth-supportive and -suppressive effects.

Membrane protein channels equipped with a cleavable linker for inducing catalysis inside nanocompartments

Precisely timed initiation of reactions and stability of the catalysts are fundamental in catalysis. We introduce here an efficient closing-opening method for nanocompartments that contain sensitive catalysts and so achieve a controlled and extended catalytic activity. We developed a chemistry-oriented approach for modifying a pore-forming membrane protein which allows for a stimuli-responsive pore opening within the membrane of polymeric nanocompartments. We synthesized a diol-containing linker that selectively binds to the pores, blocking them completely. In the presence of an external stimulus (periodate), the linker is cleaved allowing the diffusion of substrate through the pores to the nanocompartment interior where it sets off the in situ enzymatic reaction. Besides the precise initiation of catalytic activity by opening of the pores, oxidation by periodate guarantees the cleavage of the linker under mild conditions. Accordingly, this kind of responsive nanocompartment lends itself to harboring a large variety of sensitive catalysts such as proteins and enzymes.

Fostering "Education": Do Extracellular Vesicles Exploit Their Own Delivery Code?

Extracellular vesicles (EVs), comprising large microvesicles (MVs) and exosomes (EXs), play a key role in intercellular communication, both in physiological and in a wide variety of pathological conditions. However, the education of EV target cells has so far mainly been investigated as a function of EX cargo, while few studies have focused on the characterization of EV surface membrane molecules and the mechanisms that mediate the addressability of specific EVs to different cell types and tissues. Identifying these mechanisms will help fulfill the diagnostic, prognostic, and therapeutic promises fueled by our growing knowledge of EVs. In this review, we first discuss published studies on the presumed EV “delivery code” and on the combinations of the hypothesized EV surface membrane “sender” and “recipient” molecules that may mediate EV targeting in intercellular communication. Then we briefly review the main experimental approaches and techniques, and the bioinformatic tools that can be used to identify and characterize the structure and functional role of EV surface membrane molecules. In the final part, we present innovative techniques and directions for future research that would improve and deepen our understandings of EV-cell targeting.

Cleavable linkers and their application in MS-based target identification

Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.

Novel Tetrafunctional Probes Identify Target Receptors and Binding Sites of Small-Molecule Drugs from Living Systems

Significant advancement of chemoproteomics has contributed to uncovering the mechanism of action (MoA) of small-molecule drugs by characterizing drug-protein interactions in living systems. However, cell-membrane proteins such as G protein-coupled receptors (GPCRs) and ion channels, due to their low abundance and unique biophysical properties associated with multiple transmembrane domains, can present challenges for proteome-wide mapping of drug-receptor interactions. Herein, we describe the development of novel tetrafunctional probes, consisting of (1) a ligand of interest, (2) 2-aryl-5-carboxytetrazole (ACT) as a photoreactive group, (3) a hydrazine-labile cleavable linker, and (4) biotin for enrichment. In live cell labeling studies, we demonstrated that the ACT-based probe showed superior reactivity and selectivity for labeling on-target GPCR by mass spectrometry analysis compared with control probes including diazirine-based probes. By leveraging ACT-based cleavable probes, we further identified a set of representative ionotropic receptors, targeted by CNS drugs, with remarkable selectivity and precise binding site information from mouse brain slices. We anticipate that the robust chemoproteomic platform using the ACT-based cleavable probe coupled with phenotypic screening should promote identification of pharmacologically relevant target receptors of drug candidates and ultimately development of first-in-class drugs with novel MoA.

Capture and Release of Protein-Nanoparticle Conjugates by Reversible Covalent Molecular Linkers

A hybrid approach to covalently detachable molecules for nanoparticle capture and release from several custom-functionalized surfaces is described. This new surface chemistry capability provides a means for reversible binding of functionalized nanoparticles without relying on costly nucleic acid-based complexation. A new surface linker motif was devised wherein custom molecules were synthesized with components for surface anchoring, cleavage, and target capture through biotin-streptavidin binding. All capture-and-release chemistry is performed using physiological conditions (aqueous, pH 7). Covalent cleavage of linker molecules was achieved through incorporation of a tunable orthogonal reversible covalent (TORC) hydrazone functional group which underwent exchange with a competitive hydrazide aided by an aniline catalyst. The influence of the linker architecture on hydrazone exchange and nanoparticle release was probed by altering the distance between hydrazone and biotin groups using different length PEG spacers. Cleavable linkers were used to functionalize microwells, magnetic separation beads, and gold-coated glass surfaces. Upon functionalization, all surface types bound streptavidin and conjugated nanoparticles regardless of the linker structure. Conversely, the extent of hydrazone exchange as well as release of nanoparticles were influenced both by the hydrazone surface density and the linker molecular structure.

Mass-Added Density Modulation for Sorting Cells Based on Differential Surface Protein Levels

Cell sorting is a powerful tool in basic research and therapeutic enrichment. However, common cell sorting methods, such as fluorescence-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS) have significant limitations, such as generally low cell yields or restriction to binary separation, respectively. To address these limitations, we developed a two-step cell sorting method called mass-added density centrifugation (MADC) to enable nonbinary separation of large cell numbers based on surface protein levels. In the first MADC step (mass-adding), antibody-directed massive microparticles bind target surface proteins to modulate single-cell density proportionally to target protein level. Second, microparticle-laden cells are subjected to discontinuous density gradient centrifugation, whereby they separate into discrete density bands which can be isolated for downstream use. MADC will prove especially advantageous for obtaining sufficient cell numbers for protein analyses from large source populations, and it is a fast process that can facilitate live cell enrichment for therapies that require tens of millions of cells. Here, we demonstrate MADC's utility for both live and fixed cell sorts of multiple cell types based on abundance of an example target protein, CD44. CD44 quantity in separated cell groups was assayed with western blots and correlated with modulated cell density. This novel sorting method enables rapid, nonbinary isolation of large quantities of cells based on surface protein levels and should prove useful in both basic science and therapeutic applications. © 2020 International Society for Advancement of Cytometry.

Hypersensitive azobenzenes: facile synthesis of clickable and cleavable azo linkers with tunable and high reducibility

The aim of this work is to show that by increasing the number of donor substituents in a donor/acceptor system, the sensitivity of the azobenzene linkage towards a reductive cleavage reaction can be enhanced to unprecedented high levels. For instance, in a triple-donor system, less than a second constitutes the half-life of the azo (N[double bond, length as m-dash]N) bond. Synthetic access to such redox active scaffolds is highly practical and requires only 1-2 synthetic steps. The fundamental molecular design is also adaptable. This is demonstrated through scaffold functionalization by azide, tetraethylene glycol, and biotin groups. The availability of the azide group is shown in a copper-free 'click' reaction suitable in context with protein conjugation and proteomics application. Finally, the clean nature of the scission process is demonstrated with the help of liquid chromatography coupled with mass analysis. This work, therefore, describes development of cleavable azobenzene linkers that can be accessed with synthetic ease, can be multiply functionalized, and show a clean and rapid response to mild reducing conditions.

Proteomic Identification of Protein Glutathionylation in Cardiomyocytes

Reactive oxygen species (ROS) are important signaling molecules, but their overproduction is associated with many cardiovascular diseases, including cardiomyopathy. ROS induce various oxidative modifications, among which glutathionylation is one of the significant protein oxidations that occur under oxidative stress. Despite previous efforts, direct and site-specific identification of glutathionylated proteins in cardiomyocytes has been limited. In this report, we used a clickable glutathione approach in a HL-1 mouse cardiomyocyte cell line under exposure to hydrogen peroxide, finding 1763 glutathionylated peptides with specific Cys modification sites, which include many muscle-specific proteins. Bioinformatic and cluster analyses found 125 glutathionylated proteins, whose mutations or dysfunctions are associated with cardiomyopathy, many of which include sarcomeric structural and contractile proteins, chaperone, and other signaling or regulatory proteins. We further provide functional implication of glutathionylation for several identified proteins, including CSRP3/MLP and complex I, II, and III, by analyzing glutathionylated sites in their structures. Our report establishes a chemoselective method for direct identification of glutathionylated proteins and provides potential target proteins whose glutathionylation may contribute to muscle diseases.

Cysteine-reactive probes and their use in chemical proteomics

Proteomic profiling using bioorthogonal chemical probes that selectively react with certain amino acids is now a widely used method in life sciences to investigate enzymatic activities, study posttranslational modifications and discover novel covalent inhibitors. Over the past two decades, researchers have developed selective probes for several different amino acids, including lysine, serine, cysteine, threonine, tyrosine, aspartate and glutamate. Among these amino acids, cysteines are particularly interesting due to their highly diverse and complex biochemical role in our cells. In this feature article, we focus on the chemical probes and methods used to study cysteines in complex proteomes.

Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes

Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling sites are rarely verified. Here we present an enhanced chemoproteomic approach to evaluate the activity and probe reactivity of deubiquitinase enzymes, using bioorthogonally tagged ABPs and a sequential on-bead digestion protocol to enhance the identification of probe-labeling sites. We confirm probe labeling of deubiquitinase catalytic Cys residues and reveal unexpected labeling of deubiquitinases on non-catalytic Cys residues and of non-deubiquitinase proteins. In doing so, we identify ZUFSP (ZUP1) as a previously unannotated deubiquitinase with high selectivity toward cleaving K63-linked chains. ZUFSP interacts with and modulates ubiquitination of the replication protein A (RPA) complex. Our reactive-site-centric chemoproteomics method is broadly applicable for identifying the reaction sites of covalent molecules, which may expand our understanding of enzymatic mechanisms.

Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.

Applications of Reactive Cysteine Profiling

Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner. Reactive cysteines have been targeted by high-throughput screening and fragment-based ligand discovery efforts. New cysteine-reactive electrophiles and compound libraries have been synthesized to enable inhibitor discovery broadly and to minimize nonspecific toxicity and off-target activity of compounds. With the recent blockbuster success of several covalent inhibitors, and the development of new chemical proteomic strategies to broadly identify reactive, ligandable and posttranslationally modified cysteines, cysteine profiling is poised to enable the development of new potent and selective chemical probes and even, in some cases, new drugs.

Methods for the Detection, Study, and Dynamic Profiling of O-GlcNAc Glycosylation

The addition of O-linked β-N-acetylglucosamine (O-GlcNAc) to serine/threonine residues of proteins is a ubiquitous posttranslational modification found in all multicellular organisms. Like phosphorylation, O-GlcNAc glycosylation (O-GlcNAcylation) is inducible and regulates a myriad of physiological and pathological processes. However, understanding the diverse functions of O-GlcNAcylation is often challenging due to the difficulty of detecting and quantifying the modification. Thus, robust methods to study O-GlcNAcylation are essential to elucidate its key roles in the regulation of individual proteins, complex cellular processes, and disease. In this chapter, we describe a set of chemoenzymatic labeling methods to (1) detect O-GlcNAcylation on proteins of interest, (2) monitor changes in both the total levels of O-GlcNAcylation and its stoichiometry on proteins of interest, and (3) enable mapping of O-GlcNAc to specific serine/threonine residues within proteins to facilitate functional studies. First, we outline a procedure for the expression and purification of a multiuse mutant galactosyltransferase enzyme (Y289L GalT). We then describe the use of Y289L GalT to modify O-GlcNAc residues with a functional handle, N-azidoacetylgalactosamine (GalNAz). Finally, we discuss several applications of the copper-catalyzed azide-alkyne cycloaddition "click" reaction to attach various alkyne-containing chemical probes to GalNAz and demonstrate how this functionalization of O-GlcNAc-modified proteins can be used to realize (1)-(3) above. Overall, these methods, which utilize commercially available reagents and standard protein analytical tools, will serve to advance our understanding of the diverse and important functions of O-GlcNAcylation.

Versatile Platform for the Synthesis of Orthogonally Cleavable Heteromultifunctional Cross-Linkers

Cleavable and heteromultifunctional cross-linkers have proven critical in a wide range of biological applications. Traditional approaches for synthesizing these linkers suffer from various synthetic and functional limitations. In this work, an efficient sequence-defined synthetic methodology, developed for the assembly of oligothioetheramides, was used to address many of these limitations. Four heterotrifunctional cross-linkers with up to two orthogonal internal cleavage sites were synthesized. These linkers were conjugated to a pair of fluorophores that undergo Förster resonance energy transfer (FRET) and a model protein-human transferrin. Orthogonal bond cleavage was validated by mass spectrometry, fluorescent gel electrophoresis, and confocal microscopy. These studies demonstrate the versatility and biological utility of oligothioetheramides as a new class of multifunctional chemical cross-linkers and biologically relevant fluorescent probes.

Mapping the Binding Site of BMS-708163 on γ-Secretase with Cleavable Photoprobes

γ-Secretase, a four-subunit transmembrane aspartic proteinase, is a highly valued drug target in Alzheimer's disease and cancer. Despite significant progress in structural studies, the respective molecular mechanisms and binding modes of γ-secretase inhibitors (GSIs) and modulators (GSMs) remain uncertain. Here, we developed biotinylated cleavable-linker photoprobes based on the BMS-708163 GSI to study its interaction with γ-secretase. Comparison of four cleavable linkers indicated that the hydrazine-labile N-1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl (Dde) linker was cleaved most efficiently to release photolabeled and affinity-captured presenilin-1 (PS1), the catalytic subunit of γ-secretase. Peptide mapping showed that the BMS-708163-based probe photoinserted at L282 of PS1. This insertion site was consistent with the results of molecular dynamics simulations of the γ-secretase complex with inhibitor. Taken together, this work reveals the binding site of a GSI and offers insights into the mechanism of action of this class of inhibitors.

Cleavable Linkers in Chemical Proteomics Applications

The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their different chemistries, and describe how they aid in protein identification.

Target and identify: triazene linker helps identify azidation sites of labelled proteins via click and cleave strategy

A method for identifying probe modification of proteinsviatandem mass spectrometry was developed.

A Helping Hand to Overcome Solubility Challenges in Chemical Protein Synthesis

Although native chemical ligation (NCL) and related chemoselective ligation approaches provide an elegant method to stitch together unprotected peptides, the handling and purification of insoluble and aggregation-prone peptides and assembly intermediates create a bottleneck to routinely preparing large proteins by completely synthetic means. In this work, we introduce a new general tool, Fmoc-Ddae-OH, N-Fmoc-1-(4,4-dimethyl-2,6-dioxocyclo-hexylidene)-3-[2-(2-aminoethoxy)ethoxy]-propan-1-ol, a heterobifunctional traceless linker for temporarily attaching highly solubilizing peptide sequences ("helping hands") onto insoluble peptides. This tool is implemented in three simple and nearly quantitative steps: (i) on-resin incorporation of the linker at a Lys residue ε-amine, (ii) Fmoc-SPPS elongation of a desired solubilizing sequence, and (iii) in-solution removal of the solubilizing sequence using mild aqueous hydrazine to cleave the Ddae linker after NCL-based assembly. Successful introduction and removal of a Lys6 helping hand is first demonstrated in two model systems (Ebola virus C20 peptide and the 70-residue ribosomal protein L31). It is then applied to the challenging chemical synthesis of the 97-residue co-chaperonin GroES, which contains a highly insoluble C-terminal segment that is rescued by a helping hand. Importantly, the Ddae linker can be cleaved in one pot following NCL or desulfurization. The purity, structure, and chaperone activity of synthetic l-GroES were validated with respect to a recombinant control. Additionally, the helping hand enabled synthesis of d-GroES, which was inactive in a heterochiral mixture with recombinant GroEL, providing additional insight into chaperone specificity. Ultimately, this simple, robust, and easy-to-use tool is expected to be broadly applicable for the synthesis of challenging peptides and proteins.

Comprehensive mapping of O-GlcNAc modification sites using a chemically cleavable tag

The post-translational modification of serine or threonine residues of proteins with a single N-acetylglucosamine monosaccharide (O-GlcNAcylation) is essential for cell survival and function. However, relatively few O-GlcNAc modification sites have been mapped due to the difficulty of enriching and detecting O-GlcNAcylated peptides from complex samples. Here we describe an improved approach to quantitatively label and enrich O-GlcNAcylated proteins for site identification. Chemoenzymatic labelling followed by copper(i)-catalysed azide-alkyne cycloaddition (CuAAC) installs a new mass spectrometry (MS)-compatible linker designed for facile purification of O-GlcNAcylated proteins from cell lysates. The linker also allows subsequent quantitative release of O-GlcNAcylated proteins for downstream MS analysis. We validate the approach by unambiguously identifying several established O-GlcNAc sites on the proteins α-crystallin and O-GlcNAc transferase (OGT), as well as discovering new, previously unreported sites on OGT. Notably, these novel sites on OGT lie in key functional domains of the protein, underscoring how this site identification method may reveal important biological insights into protein activity and regulation.

An isotopically tagged azobenzene-based cleavable linker for quantitative proteomics

Putting a number on it: Cleavable linkers are widely utilized in proteomics applications. In particular, the azobenzene-based linker cleaves under mild conditions that are mass-spectrometry-compatible. Here, we adapt this linker for quantitative proteomic applications by incorporating an isotopic label. These light- and heavy-tagged linkers enable the identification and quantitation of labeled peptides from multiple proteomes.