Activity-based probes for protein tyrosine phosphatases

Abstract

Protein tyrosine phosphatases (PTPs) are involved in the regulation of many aspects of cellular activity including proliferation, differentiation, metabolism, migration, and survival. Given the large number and complexity of PTPs in cell signaling, new strategies are needed for the integrated analysis of PTPs in the whole proteome. Unfortunately, the activities of many PTPs are tightly regulated by posttranslational mechanisms, limiting the utility of standard genomics and proteomics methods for functional characterization of these enzymes. To facilitate the global analysis of PTPs, we designed and synthesized two activity-based probes that consist of ␣-bromobenzylphosphonate as a PTP-specific trapping device and a linker that connects the trapping device with a biotin tag for visualization and purification. We showed that these probes are active site-directed irreversible inactivators of PTPs and form a covalent adduct with PTPs involving the active site Cys residue. Additionally, we demonstrated that the probes are extremely specific toward PTPs while remaining inert to other proteins, including the whole proteome from Escherichia coli. Consequently, these activity-based PTP probes can be used to profile PTP activity in complex proteomes. The ability to interrogate the entire PTP family on the basis of changes in their activity should greatly accelerate both the assignment of PTP function and the identification of potential therapeutic targets. P rotein tyrosine phosphatases (PTPs) constitute a large family of signaling enzymes (Ͼ100 in humans) that are important for the regulation of cell proliferation, differentiation, metabolism, migration, and survival (1, 2). Dysfunction in PTPs results in aberrant Tyr phosphorylation, which has been linked to the etiology of several human diseases, including cancer and diabetes (3, 4). Unlike protein kinases, of which Tyr-and Ser͞Thr-specific kinases share sequence identity, the PTPs show no sequence similarity with Ser͞Thr phosphatases or the broad-specificity phosphatases, such as acid or alkaline phosphatases. The hallmark that defines the PTP superfamily is the active site amino acid sequence C(X) 5 R, also called the PTP signature motif, in the catalytic domain. The PTPs can be broadly divided into two groups based on active site substrate specificity: the Tyr-specific and the dual-specificity phosphatases, which hydrolyze pSer͞Thr as well as pTyr. Despite variations in primary structure and differences in substrate specificity, key structural features in the active site and the mechanism of catalysis are conserved among all members of the PTP superfamily (5, 6).Although PTPs share a common catalytic mechanism, they have distinct (and often unique) biological functions in vivo. One of the major challenges in the field is to rapidly establish functional roles for PTPs, in both normal physiology and pathogenic conditions. Gene knockout analysis is useful in assessing the role of a number of PTPs in cellular signaling. However, this process is often tedious, and gene a...

Mechanistic Analysis of a Suicide Inactivator of Histone Demethylase LSD1

“…The use of affinity labels and mechanism-based inactivators in proteomics analysis has undergone a renaissance with the advent of modern mass spectrometric and chromatographic techniques (40)(41)(42)(43). Excellent probes have been developed for proteases, phosphatases, and protein arginine deiminases based on electrophilic reactivity.…”

Aryl Vinyl Sulfonates and Sulfones as Active Site-Directed and Mechanism-Based Probes for Protein Tyrosine Phosphatases

“…At appropriate time intervals, aliquots of 2 µl were removed from the reaction and added into a 200 µl solution containing 20 mM pNPP in pH 6.0 buffer at 30 °C. 14 The kinetic parameters of the inactivation reaction were obtained by fitting the data to the following equations: …”

“…14 The 12-14 fold higher affinity exhibited by PVSN and PVS for the PTP active site indicates that they are superior pTyr surrogates. Second, α-bromobenzyl phosphonate undergoes significant solvolysis at pH greater than 7 14 , whereas PVSN and PVS are chemically inert under similar conditions, even in the presence of 1 mM glutathione ( Figures S2 & S3). Third, like most pTyr mimetics, α-bromobenzyl phosphonate is negatively charged and exhibits exceedingly low membrane permeability.…”

A modified cysteinyl-labeling assay reveals reversible oxidation of protein tyrosine phosphatases in angiomyolipoma cells

“…During this phase, cyclic sulfenamide and sulfenic acid forms of the active-site Cys residues, which were protected from alkylation in the previous step, were reduced back to their thiolate states. After this crucial step, the lysates were incubated with biotinylated BBP (16) or IAP probes (1 mM, 5 mM) for 1 h on a shaker at room temperature. Biotinylated proteins were enriched by using streptavidin-Sepharose beads for 16 h at 4°C on a rotating wheel, with sequential rounds of centrifugation (12,000 ϫ g, 1 min, 4°C) using PBS to wash the beads.…”

“…The BBP probe is a phosphonate-based molecule that has been shown to display specificity toward PTPs (16). Unlike the IAP probe, which forms a stable thioether bond with the reactive thiol group, BBP interacts with the PTP active site as would a phosphorylated tyrosyl residue in a substrate and forms a nonhydrolyzable cysteinyl-phosphate bond (16). Therefore, the specificity of the probes was assessed in each of the cell populations.…”