Chemistry-based functional proteomics to identify novel deubiquitylating enzymes involved in viral infection

Ubiquitylation is a reversible post-translational modification pathway that regulates a variety of cellular processes including protein degradation and trafficking, intracellular localization, DNA repair, immune response and cellcycle progression. Deubiquitylating enzymes (DUBs) can remove the ubiquitin from the modified proteins and reverse the ubiquitylation-induced biological processes; hence it isn't hard to understand that viral pathogens take advantage of the host cell ubiquitin system through disturbing DUBs, for infection and replication. Although accumulated virus-related DUBs have been defined, but how viruses regulate their expression and activities is poor understand because of limitation of technologies. Recently, chemistry-based functional proteomics, which can not only monitor the alteration of abundance but also changes in activity of enzymes, was used to study the function of DUBs involved in virus infection and held much promise. Theses works suggest that chemistry-based functional proteomics is a potent strategy for high throughput screening of virus-related DUBs and exploring their roles in virus infection.     

A tandem orthogonal proteolysis strategy for high-content chemical proteomics

The field of proteomics aims to assign functions to the numerous protein products encoded by eukaryotic and prokaryotic genomes. Toward this end, chemical strategies have emerged as a powerful means to enrich specific classes of proteins based on shared functional properties, such as catalytic activity [activity-based protein profiling (ABPP)], and post-translational modification state. The theoretical information content in chemical proteomic experiments greatly exceeds the actual data procured, due in large part to limitations in existing analytical technologies. Here, we present a tandem orthogonal proteolysis (TOP) strategy for high-content chemical proteomics that enables the parallel characterization of probe-labeled proteins and sites of probe modification. The TOP approach exploits "click chemistry" to introduce a multifunctional tag onto probe-labeled proteins that contains both a biotin group for protein enrichment and a tobacco etch virus (TEV) protease cleavage site for selective release of probe-modified peptides. Following capture on streptavidin beads, protein targets of probes and their sites of labeling are sequentially identified by a two-step proteolysis strategy (trypsin and TEV, respectively). We apply the TOP method to characterize targets of sulfonate ester ABPP probes in tissue proteomes, resulting in the discovery of numerous active site-labeled enzymes. Enzymes modified on regulatory sites and proteins of unknown function were also identified. These findings indicate that a wide range of functional residues are targeted by sulfonate ester probes and highlight the value of TOP-based chemical proteomics for the characterization of proteins and the residues that regulate their activity.     

基于化学蛋白质组学的药物靶标鉴定

通过药物靶标鉴定,可以建立药物活性与细胞表型之间的联系,阐明药物的作用机理,还可以发现药物的脱靶效应和耐药性机制,发现治疗药物的新靶点,并在药物开发的早期阶段预测可能存在的毒性,降低药物研发失败的风险。目前虽然科学技术取得了飞速发展,但是鉴定药物靶标依然是一件令人生畏的工作。本文对近10年来药物靶标鉴定方面的研究进展,特别是无化学标记的新技术进行了评述。     

Activity-based fingerprinting and inhibitor discovery of cysteine proteases in a microarray

A panel of 20 peptide vinyl sulfone probes has been synthesized and used to generate activity-based fingerprinting profiles of cysteine proteases in both gel- and microarray-based formats; the inhibitor fingerprints of representative small molecule inhibitors targeted against 4 cysteine proteases were also obtained, in high-throughput, using the same protein microarray platform.     

Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics

The advances in bioorthogonal ligation methods have provided new opportunities for proteomic analysis of newly synthesized proteins, posttranslational modifications, and specific enzyme families using azide/alkyne-functionalized chemical reporters and activity-based probes. Efficient enrichment and elution of azide/alkyne-labeled proteins with selectively cleavable affinity tags are essential for protein identification and quantification applications. Here, we report the synthesis and comparative analysis of Na?S?O?-cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. We demonstrated that ortho-hydroxyl substituent is required for efficient azobenzene-bond cleavage and show that these cleavable affinity tags can be used to identify newly synthesized proteins in bacteria targeted by amino acid chemical reporters as well as their sites of modification on endogenously expressed proteins. The azobenzene-based affinity tags are compatible with in-gel, in-solution, and on-bead enrichment strategies and should afford useful tools for diverse bioorthogonal proteomic applications.     

Activity-based profiling for drug discovery

Activity-based protein profiling (ABPP) is emerging as a game-changing tool for drug discovery, target validation, and basic biology. In this issue, Chang et?al. (2011) report the ABPP-facilitated discovery of JW480, a highly selective potent and orally bioavailable inhibitor of monoalkylglycerol ether hydrolase KIAA1363 that dramatically impairs in?vivo growth of human prostate cancer cell lines.     

Immobilized enzymes in chemical analysis

Immobilization of enzymes has proved to be useful in stabilizing them, in retrieving and reusing them, and in producing unstable or expensive reagents. Specific technologies have been developed for analytical applications of immobilized enzymes, including probes (e.g., enzyme electrodes) and reactors. The characteristics of these devices and their advantages and disadvantages will be presented.     

Activity-based probe for histidine kinase signaling

Bacterial two-component systems (TCSs) are signaling pathways composed of two proteins: a histidine kinase (HK) and a response regulator (RR). Upon stimulation, the HK autophosphorylates at a conserved histidine. The phosphoryl group is subsequently transferred to an aspartate on an RR, eliciting an adaptive response, often up- or downregulation of gene expression. TCS signaling controls many functions in bacteria, including development, virulence, and antibiotic resistance, making the proteins involved in these systems potential therapeutic targets. Efficient methods for the profiling of HKs are currently lacking. For direct readout of HK activity, we sought to design a probe that enables detection of the phosphotransfer event; however, analysis of the phosphohistidine species is made difficult by the instability of the P-N bond. We anticipated that use of a γ-thiophosphorylated ATP analogue, which would yield a thiophosphorylated histidine intermediate, could overcome this challenge. We determined that the fluorophore-conjugated probe, BODIPY-FL-ATPγS, labels active HK proteins and is competitive for the ATP binding site. This activity-based probe provides a new strategy for analysis of TCSs and other HK-mediated processes and will facilitate both functional studies and inhibitor identification.     

AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics

Target identification remains challenging for the field of chemical biology. We describe an integrative chemical genomic and proteomic approach combining the use of differentially active analogs of small molecule probes with stable isotope labeling by amino acids in cell culture-mediated affinity enrichment, followed by subsequent testing of candidate targets using RNA interference-mediated gene silencing. We applied this approach to characterizing the natural product K252a and its ability to potentiate neuregulin-1 (Nrg1)/ErbB4 (v-erb-a erythroblastic leukemia viral oncogene homolog 4)-dependent neurotrophic factor signaling and neuritogenesis. We show that AAK1 (adaptor-associated kinase 1) is a relevant target of K252a, and that the loss of?AAK1?alters ErbB4 trafficking and expression levels,?providing evidence for a previously unrecognized role for AAK1 in Nrg1-mediated neurotrophic?factor signaling. Similar strategies should lead to the discovery of novel targets for therapeutic development.     

Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions

Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein-protein interactions involved in essentially every cellular process. While significant progress has been made to detect PTMs, profiling protein-protein interactions mediated by these PTMs remains a challenge. Here, we report a method that combines a photo-cross-linking strategy with stable isotope labeling in cell culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent protein-protein interactions. To develop and apply this approach, we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me(3)), a PTM linked to actively transcribed gene promoters. Our approach identified proteins previously known to recognize this modification and MORC3 as a new protein that binds H3M4Me(3). This study indicates that our cross-linking-assisted and SILAC-based protein identification (CLASPI) approach can be used to profile protein-protein interactions mediated by PTMs, such as lysine methylation.     

A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics

The identification of individual protein species within an organism's proteome has been optimised by increasing the information produced from mass spectral analysis through the chemical derivatisation of tryptic peptides and the development of new software tools. Peptide fragments are subjected to two forms of derivatisation. First, lysine residues are converted to homoarginine moieties by guanidination. This procedure has two advantages, first, it usually identifies the C-terminal amino acid of the tryptic peptide and also greatly increases the total information content of the mass spectrum by improving the signal response of C-terminal lysine fragments. Second, an Edman-type phenylthiocarbamoyl (PTC) modification is carried out on the N-terminal amino acid. The renders the first peptide bond highly susceptible to cleavage during mass spectrometry (MS) analysis and consequently allows the ready identification of the N-terminal residue. The utility of the procedure has been demonstrated by developing novel bioinformatic tools to exploit the additional mass spectral data in the identification of proteome proteins from the yeast Saccharomyces cerevisiae. With this combination of novel chemistry and bioinformatics, it should be possible to identify unambiguously any yeast protein spot or band from either two-dimensional or one-dimensional electropheretograms.     

Cryptic functions of enzymes in chemical catalysis

Using a number of examples, this article demonstrates how the functional groups responsible for the catalytic activity of an enzyme must be studied within the context of the enzyme-substrate complex. Very often a substrate will actively cooperate with the enzyme to bring about its own transformation. The so-called cryptic functions of enzymes are considered in the case of seryl proteases which, according to the type of substrate or structural modification introduced in the enzyme, may exhibit esterase, amidase, protease, racemase or dehydratase activity. The cryptic functions may possess a physiological significance which reflects the evolutionary history of the protein. Alternatively they may offer a simple way of exploiting the enzymes as catalysts capable of taking part in the chemical reactions of biotechnological interest but little physiological importance.This work is dedicated to Prof.E. Wünsch (München) at the occasion of his 60^th birthday.     

Use of immobilized enzymes in chemical analysis

Immobilized enzymes are becoming increasingly popular as analytical reagents because of their reusability, stability, and sensitivity to many inhibitors that would seriously interfere in assays using soluble enzymes. In this article, some of the kinetic and catalytic effects of immobilized enzymes in analysis will be discussed. The shift of the activity-pH profile curves on immobilization, the changes in temperature dependence, the inhibitor constants (K_i), Michaelis constants (K_m), and the maximum velocity ( V_max), plus others, will be discussed. Finally, the use of these immobilized enzymes in fluorometric and electrochemical monitoring systems will be shown, and the future of these reagents in various areas will be discussed. A survey of enzyme electrodes will be presented as an example of the use of immobilized enzymes. Application of immobilized enzyme technology to the assay of BUN, glucose, uric acid, amino acids, ethanol, and other metabolites will be discussed.     

Enantioselective reactions catalyzed by synthetic enzymes. A model for chemical evolution

Polyleucines of various lengths act as enantioselective catalysts in the aldol condensation between cyclohexanone and various aromatic aldehydes. Polyleucine and other polyamino acids behave as synthetic enzymes in the epoxidation of chalcone and other electron-deficient alkenes. Both reactions are of considerable prebiotic significance.     

Inferring the chemical mechanism from structures of enzymes

Chemistry has once again embraced the study of enzyme mechanism as a core discipline. Chemists are uniquely able to contribute to the analysis of enzymes through their understanding of the reactivity of atoms. In this tutorial review for the Corday-Morgan medal, I will concentrate on the work from my lab over the past six years. I discuss enzymes which transform carbohydrates and incorporate halogens. The tutorial review will emphasise the strengths and limitations of structural biology as a means to deducing the chemical mechanism.     

Synthesis of a new hydrophilic o-nitrobenzyl photocleavable linker suitable for use in chemical proteomics

Linkers currently used in solid phase synthesis are generally short and hydrophobic, limiting their usefulness in biological systems. Herein, we describe a facile synthesis of a long, hydrophilic, o-nitrobenzyl photocleavable linker, suitable for constructing affinity supports for use in chemical proteomics. The rates of photolysis of the linker on exposure to UV light emitting diodes are reported.