Tyrosine Residues In Proteins Research Articles

Tyrosine-Reactive Cross-Linker for Probing Protein Three-Dimensional Structures.

Cross-linking mass spectrometry (XL-MS) has made significant progress in understanding the structure of protein and elucidating architectures of larger protein complexes. Current XL-MS applications are limited to targeting lysine, glutamic acid, aspartic acid, and cysteine residues. There remains a need for the development of novel cross-linkers enabling selective targeting of other amino acid residues in proteins. Here, a novel simple cross-linker, namely, [4,4'-(disulfanediylbis(ethane-2,1-diyl)) bis(1,2,4-triazolidine-3,5-dione)] (DBB), has been designed, synthesized, and characterized. This cross-linker can react selectively with tyrosine residues in protein through the electrochemical click reaction. The DBB cross-links produced the characteristic peptides before and after electrochemical reduction, thus permitting the simplified data analysis and accurate identification for the cross-linked products. This is the first time a cross-linker is developed for targeting tyrosine residues on protein without using photoirradiation or a metal catalyst. This strategy might potentially be used as a complementary tool for XL-MS to probe protein 3D structures, protein complexes, and protein-protein interaction.

UV Radiation-induced Impairment of Cellular Morphology and Motility is Enhanced by DUSP3/VHR Loss and FAK Activation.

DUSP3 is a phosphatase expressed and active in several tissues that dephosphorylates tyrosine residues in many regulatory proteins of cellular activities such as proliferation, survival, and cell death. Recently, two new independent functions were assigned to this enzyme: dephosphorylation of focal adhesion kinase (FAK) and regulation of nucleotide-excision repair (NER) pathway. Genotoxic stress by UV radiation is known to affect cell morphology, adhesion, and migration for affecting, for example, the Rho GTPases that regulate actin cytoskeleton. This work investigated the intersection of DUSP3 function, XPA protein activity, and UV toxicity by examining cell migration, FAK, and SRC kinase phosphorylation status, in addition to cell morphology, in fibroblast cells proficient (MRC-5) or deficient (XPA) of the NER pathway. DUSP3 loss reduced cell migration of normal cells, which was stimulated by the genotoxic stress, effects evidenced in presence of serum mitogenic stimulus. However, NER-deficient cells migration response was the opposite since DUSP3 loss increased migration, especially after cells being exposed to UV stress. The levels of pFAK(Y397) peaked 15 min and 1 h after UV radiation in normal cells, but only slightly increased in repair-deficient cells. However, the DUSP3 knockdown strongly raised pFAK(Y397) levels in both cells, but especially in XPA cells as supported by the higher SRC activity. These effects impacted on the dynamics of actin-based structures formation, such as stress fibres, apparently dependent on DUSP3 and DNA-repair (NER) proficiency of the cells. Altogether our findings suggest this dual-phosphatase is bridging gaps between the complex regulation of cell morphology, motility, and genomic stability.

Protein immobilization on polyvinylphenol via tyrosine oxidation of proteins catalyzed by horseradish peroxidase

AbstractSurface functionalization of polymeric materials holds great potential in biological and medical fields with the aim toward realizing desired biological reactions (e.g., cell adhesion, and immune response), especially for proteins which have physiological functions. The objective was to examine characteristics of a unique and facile protein immobilization on a phenol‐containing polymeric material utilizing horseradish peroxidase (HRP) and tyrosine residues of target proteins as catalyst and substrates, respectively. Cy3‐labeled streptavidin exhibited the predicted immobilization behavior since the reaction effectively proceeded in the presence of HRP‐H2O2 and on the surface of polyvinylphenol. This procedure was applicable to other representative proteins, that is, bovine serum albumin, immunoglobulin G (IgG), and HRP as substrates. However, IgG exhibited anomalous reaction behavior under the present reaction condition probably due to its rich tyrosine content. Undesired immobilization of HRP was minimized by addition of large amounts of a competitive substrate. The biotin‐binding affinity of streptavidin‐immobilized surface was confirmed to maintain activity even after the immobilization procedure.

Cross-linking and modification of fibronectin by peroxynitrous acid: Mapping and quantification of damage provides a new model for domain interactions

Fibronectin (FN) is an abundant glycoprotein found in plasma and the extracellular matrix (ECM). It is present at high concentrations at sites of tissue damage, where it is exposed to oxidants generated by activated leukocytes, including peroxynitrous acid (ONOOH) formed from nitric oxide (from inducible nitric oxide synthase) and superoxide radicals (from NADPH oxidases and other sources). ONOOH reacts rapidly with the abundant tyrosine and tryptophan residues in ECM proteins, resulting in the formation of 3-nitrotyrosine, di-tyrosine, and 6-nitrotryptophan. We have shown previously that human plasma FN is readily modified by ONOOH, but the extent and location of modifications, and the role of FN structure (compact versus extended) in determining these factors is poorly understood. Here, we provide a detailed LC-MS analysis of ONOOH-induced FN modifications, including the extent of their formation and the sites of intramolecular and intermolecular cross-links, including Tyr-Tyr, Trp-Trp, and Tyr-Trp linkages. The localization of these cross-links to specific domains provides novel data on the interactions between different modules in the compact conformation of plasma FN and allows us to propose a model of its unknown quaternary structure. Interestingly, the pattern of modifications is significantly different to that generated by another inflammatory oxidant, HOCl, in both extent and sites. The characterization and quantification of these modifications offers the possibility of the use of these materials as specific biomarkers of ECM modification and turnover in the many pathologies associated with inflammation-associated fibrosis.

Monitoring peptide tyrosine nitration by spectroscopic methods.

Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870cm-1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation.

Peroxynitrite-Mediated Structural Changes in Histone H2A: Biochemical and Biophysical Analysis.

Peroxynitrite, a nitrating and oxidizing agent, is formed by the interaction between nitric oxide and superoxide radicals. H2A histone is a basic nucleoprotein and is one of the major core histones responsible for packaging DNA. It has been shown that they are highly sensitive to oxidizing and nitrating agents. Nitration of tyrosine residues in proteins by peroxynitrite is regarded as a marker of nitrosative damage. The dityrosine bond, an oxidative covalent cross-link between two tyrosines in protein, is increasingly identified as a marker of oxidative stress, aging and neurodegerative diseases. Peroxinitrite-mediated nitration and dinitration in H2A histone was assessed by various biophysical techniques. The data presented in this study showed that the dityrosine content was found to be elevated in H2A histone modified with peroxynitrite. The formation of dityrosine showed a decrease in fluorescence intensity, generation of a new peak in FT-IR, increase in hydrodynamic size, and loss of secondary and tertiary structure of H2A resulting in a partially folded structure. We report that H2A may undergo conformational and structural changes under nitrosative and oxidative stress from the deleterious effects of peroxynitrite.

Immunopharmacology and Quantitative Analysis of Tyrosine Kinase Signaling.

In this article we describe the use of pharmacological and genetic tools coupled with immunoblotting (Western blotting) and targeted mass spectrometry to quantify immune signaling and cell activation mediated by tyrosine kinases. Transfer of the ATP γ phosphate to a protein tyrosine residue activates signaling cascades regulating the differentiation, survival, and effector functions of all cells, with unique roles in immune antigen receptor, polarization, and other signaling pathways. Defining the substrates and scaffolding interactions of tyrosine kinases is critical for revealing and therapeutically manipulating mechanisms of immune regulation. Quantitative analysis of the amplitude and kinetics of these effects is becoming ever more accessible experimentally and increasingly important for predicting complex downstream effects of therapeutics and for building computational models. Secondarily, quantitative analysis is increasingly expected by reviewers and journal editors, and statistical analysis of biological replicates can bolster claims of experimental rigor and reproducibility. Here we outline methods for perturbing tyrosine kinase activity in cells and quantifying protein phosphorylation in lysates and immunoprecipitates. The immunoblotting techniques are a guide to probing the dynamics of protein abundance, protein–protein interactions, and changes in post‐translational modification. Immunoprecipitated protein complexes can also be subjected to targeted mass spectrometry to probe novel sites of modification and multiply modified or understudied proteins that cannot be resolved by immunoblotting. Together, these protocols form a framework for identifying the unique contributions of tyrosine kinases to cell activation and elucidating the mechanisms governing immune cell regulation in health and disease. © 2020 The Authors. Basic Protocol 1: Quantifying protein phosphorylation via immunoblotting and near‐infrared imaging Alternate Protocol: Visualizing immunoblots using chemiluminescence Basic Protocol 2: Enriching target proteins and isolation of protein complexes by immunoprecipitation Support Protocol: Covalent conjugation of antibodies to functionalized beads Basic Protocol 3: Quantifying proteins and post‐translational modifications by targeted mass spectrometry

The intrinsic apoptotic pathway lies upstream of oxidative stress in multiple organs

Oxidative stress increases with age in multiple organ systems and is implicated in the development of age-related pathologies in them. Studies from our laboratory show that the intrinsic pathway proapoptotic proteins BAX and caspase-3 (CASP3) lie upstream of mitochondrial production of oxidative stress-inducing reactive species (RS) such as reactive oxygen and reactive nitrogen species (ROS and RNS) in apoptotic and nonapoptotic neurons in cell culture. Our objective in this study was to determine if these findings could be generalized to the development of oxidative stress in nonneuronal tissues in vivo. We first investigated the effect of genetic deletion of Bax on DNA damage in the liver, heart and kidneys of female mice of increasing ages (5, 14, 22 months). The organs of the aged mice showed increased oxidative DNA strand breaks compared to young animals (5 month). Ablation of Bax greatly reduced this damage. We next assessed lipid peroxidation, DNA oxidation, and protein tyrosine nitration to determine whether Casp3 deletion reduces oxidative stress in the hearts, livers, and kidneys of 12-month-old female mice. Lipid peroxides and 8-hydroxy-2’-deoxyguanosine (8-OHdG) levels were much lower in organs from mice with depleted Casp3 than in those of wild type animals. Nitration of protein tyrosine residues, caused by RNS, was also significantly suppressed in the tissues of Casp3 null mice compared to those in wild type mice. Our findings indicate that BAX and CASP3 have a vital role in the generation of oxidative stress in organs of aged mice.

Discriminating changes in protein structure using tyrosine conjugation.

Chemical modification of proteins has been crucial in engineering protein-based therapies, targeted biopharmaceutics, molecular probes, and biomaterials. Here, we explore the use of a conjugation-based approach to sense alternative conformational states in proteins. Tyrosine has both hydrophobic and hydrophilic qualities, thus allowing it to be positioned at protein surfaces, or binding interfaces, or to be buried within a protein. Tyrosine can be conjugated with 4-phenyl-3H-1,2,4-triazole-3,5(4H)-dione (PTAD). We hypothesized that individual protein conformations could be distinguished by labeling tyrosine residues in the protein with PTAD. We conjugated tyrosine residues in a well-folded protein, bovine serum albumin (BSA), and quantified labeled tyrosine with liquid chromatography with tandem mass spectrometry. We applied this approach to alternative conformations of BSA produced in the presence of urea. The amount of PTAD labeling was found to relate to the depth of each tyrosine relative to the protein surface. This study demonstrates a new use of tyrosine conjugation using PTAD as an analytic tool able to distinguish the conformational states of a protein.

Analysis of the glycosylation products of peanut protein and lactose by cold plasma treatment: Solubility and structural characteristics

Cold plasma (CP) treatment was used to prepare the glycosylation conjugates of high-temperature peanut protein isolate (HPPI) and lactose to improve the solubility of HPPI. We observed that by increasing the CP treatment time to 3 min, the solubility of the conjugates increased to 1.34 mg/mL. An increase in the degree of glycosylation and a decrease in the degree of browning indicated that although CP treatment accelerated the glycosylation of HPPI and lactose, it interfered with the formation of melanoidin. The analysis of protein tertiary structure showed that tryptophan and tyrosine residues in proteins undergoing CP treatment were the primary sites for the Maillard reaction. The relative decrease in surface hydrophobicity and FT-IR analysis indicated that the increase in the -OH stretching vibration intensity on the protein surface represented the formation of the covalent bonds between HPPI and lactose during the CP treatment. An increase in the denaturation temperature of proteins was observed after grafting with lactose. Changes in the secondary structure and surface structure of proteins showed that lactose covalently bonded to the surface of HPPI during CP treatment, forming a more stable ordered structure.

Binding Affinities Studies of Nitrated Model Peptides to Monoclonal Anti-3-nitrotyrosine Antibody

Tyrosine nitration has been shown to be an important oxidative protein modification and play a crucial role in pathophysiological conditions, associated with oxidative stress, such as atherosclerosis and neurodegenerative disease. For a better understanding of nitration mechanism, the identification and the quantification of nitration sites represents an important research goal. Due to (i) the low levels of nitration in native proteins, (ii) structural changes induced by nitration and (iii) the specificity of anti � 3 nitro tyrosine antibodies the method which may provide the identification of nitration sites in proteins represent a challenging experimental task. In this work we have used synthetic nitrated tyrosine containing peptides to determine antibody-binding affinities and specificity of different tyrosine residue (Tyr33, Tyr98, Tyr107and Tyr122) in Eosinophil cationic proteins (ECP). The highest affinity of nitrated ECP peptides to the monoclonal antibody (anti-3NT) was obtained for the only in vivo nitrated identified residue Tyr33(0.082 �M); in contrast, all other three nitrated residues at Tyr98, Tyr107 and Tyr122) showed significant lower affinity being imbedded in the ECP protein structure as similar resulted by molecular computational modeling.

Efficient Site-Specific Prokaryotic and Eukaryotic Incorporation of Halotyrosine Amino Acids into Proteins.

Post-translational modifications (PTMs) of protein tyrosine (Tyr) residues can serve as a molecular fingerprint of exposure to distinct oxidative pathways and are observed in abnormally high abundance in the majority of human inflammatory pathologies. Reactive oxidants generated during inflammation include hypohalous acids and nitric oxide-derived oxidants, which oxidatively modify protein Tyr residues via halogenation and nitration, respectively, forming 3-chloroTyr, 3-bromoTyr, and 3-nitroTyr. Traditional methods for generating oxidized or halogenated proteins involve nonspecific chemical reactions that result in complex protein mixtures, making it difficult to ascribe observed functional changes to a site-specific PTM or to generate antibodies sensitive to site-specific oxidative PTMs. To overcome these challenges, we generated a system to efficiently and site-specifically incorporate chloroTyr, bromoTyr, and iodoTyr, and to a lesser extent nitroTyr, into proteins in both bacterial and eukaryotic expression systems, relying on a novel amber stop codon-suppressing mutant synthetase (haloTyrRS)/tRNA pair derived from the Methanosarcina barkeri pyrrolysine synthetase system. We used this system to study the effects of oxidation on HDL-associated protein paraoxonase 1 (PON1), an enzyme with important antiatherosclerosis and antioxidant functions. PON1 forms a ternary complex with HDL and myeloperoxidase (MPO) in vivo. MPO oxidizes PON1 at tyrosine 71 (Tyr71), resulting in a loss of PON1 enzymatic function, but the extent to which chlorination or nitration of Tyr71 contributes to this loss of activity is unclear. To better understand this biological process and to demonstrate the utility of our GCE system, we generated PON1 site-specifically modified at Tyr71 with chloroTyr and nitroTyr in Escherichia coli and mammalian cells. We demonstrate that either chlorination or nitration of Tyr71 significantly reduces PON1 enzymatic activity. This tool for site-specific incorporation of halotyrosine will be critical to understanding how exposure of proteins to hypohalous acids at sites of inflammation alters protein function and cellular physiology. In addition, it will serve as a powerful tool for generating antibodies that can recognize site-specific oxidative PTMs.

Radiometal-Containing Aryl Diazonium Salts for Chemoselective Bioconjugation of Tyrosine Residues.

Tyrosine is an attractive target for chemo- and site-selective protein modification. The particular chemical nature of tyrosine residues allows bioconjugation chemistry with reactive aryl diazonium salts via electrophilic aromatic substitution to produce diazo compounds. In this work, we describe the preparation of 64Cu- and 68Ga-labeled 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA)-diazonium salts as building blocks for azo coupling chemistry with tyrosine and tyrosine-containing peptides and proteins under mild conditions. 2-S-(4-aminobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (p-NH2-Bn-NOTA) was used to form the corresponding 64Cu- and 68Ga-labeled complexes, followed by diazotization with NaNO2 in the presence of HCl. 64Cu- and 68Ga-labeled NOTA complexes were prepared in high radiochemical yields >80% starting from 20 μg of p-NH2-Bn-NOTA. Conversion of p-NH2-Bn-NOTA complexes into diazonium salts followed by azo coupling with l-tyrosine afforded 64Cu- and 68Ga-labeled tyrosine in radiochemical yields of 80 and 56%, respectively. Azo coupling with tyrosine-containing hexapeptide neurotensin NT(8–13) afforded 64Cu- and 68Ga-labeled NT(8–13) in radiochemical yields of 45 and 11%, respectively. Azo coupling of 64Cu-labeled NOTA-diazonium salt with human serum albumin (HSA) gave 64Cu-labeled HSA in radiochemical yields of 20%. The described azo coupling chemistry represents an innovative and versatile bioconjugation strategy for selective targeting of tyrosine residues in peptides and proteins.

Mechanistic insight into the catalytic inhibition by nitroxides of tyrosine oxidation and nitration

BackgroundNitroxide antioxidants (RNO•) protect from injuries associated with oxidative stress. Tyrosine residues in proteins are major targets for oxidizing species giving rise to irreversible cross-linking and protein nitration, but the mechanisms underlying the protective activity of RNO• on these processes are not sufficiently clear. MethodsTyrosine oxidation by the oxoammonium cation (RN+=O) was studied by following the kinetics of RNO• formation using EPR spectroscopy. Tyrosine oxidation and nitration were investigated using the peroxidase/H2O2 system without and with nitrite. The inhibitory effect of RNO• on these processes was studied by following the kinetics of the evolved O2 and accumulation of tyrosine oxidation and nitration products. ResultsTyrosine ion is readily oxidized by RN+=O, and the equilibrium constant of this reaction depends on RNO• structure and reduction potential. RNO• catalytically inhibits tyrosine oxidation and nitration since it scavenges both tyrosyl and •NO2 radicals while recycling through RN+=O reduction by H2O2, tyrosine and nitrite. The inhibitory effect of nitroxide on tyrosine oxidation and nitration increases as its reduction potential decreases where the 6-membered ring nitroxides are better catalysts than the 5-membered ones. ConclusionsNitroxides catalytically inhibit tyrosine oxidation and nitration. The proposed reaction mechanism adequately fits the results explaining the dependence of the nitroxide inhibitory effect on its reduction potential and on the concentrations of the reducing species present in the system. General significanceNitroxides protect against both oxidative and nitrative damage. The proposed reaction mechanism further emphasizes the role of the reducing environment to the efficacy of these catalysts.

1333-P: Increased Spare Respiratory Capacity in Circulating Cells and Decreased Serum Antioxidant Defense Mechanisms in Obese Children

With increasing rates of childhood obesity, diagnoses of insulin resistance and type 2 diabetes (DM) in children is on the rise. Mitochondrial dysfunction is associated with insulin resistance and DM, therefore bioenergetics profiling of circulating cells may serve as a marker for mitochondrial dysfunction in insulin resistant subjects. The advantage of this biomarker is that others currently in use may not exhibit alterations until symptoms are already present. Mitochondrial bioenergetics (Seahorse XF96) was measured in peripheral blood mononuclear cells (PBMCs) and platelets. Levels of oxidative stress, post-translational modifications of protein tyrosine residues, 3-Nitrotyrosine and 3-Chlorotyrosine, reduced (GSH) and oxidized (GSSG) glutathione, as well as whole-body D31-palmitate oxidation were also assessed in healthy lean (HL; n=18), and overweight/obese (OW/OB; n=29) (BMI ≥85th percentile) 5-9 years old children. While maximal respiration was not different, the reserve capacity (RC) was increased in OW/OB compared to HL subjects in PBMC (45,6±4,7 vs. 32,1±7.7; p=0.05) and platelet (65,3±3.7 vs. 31,2±6,7; p=0.001). Importantly, 20% of these children already presented HbA1c levels above 6.5%. Moreover, 3-Chlorotyrosine was elevated (52,0±3,1 vs. 40,7±1,8; p=0.05), while GSH/GSSG and cysteine/cysteine (intracellular, extracellular redox buffers, respectively) tended to be decreased. Palmitate oxidation is being quantified. RC is a critical component of the cell’s bioenergetics and can be used during increases in energy demand. Our results suggest significant metabolic adjustments to an excess in substrate availability and already compromised antioxidant defenses in 5-9 year old OW/OB children. Oxidative stress and damage occur when antioxidant defense mechanisms fail to counter-balance and control reactive oxygen species generated from endogenous oxidative metabolism or from pro-oxidant environmental exposures. Disclosure E. Carvalho: None. S. Rose: None. M. Cotter: None. S.C. Bennuri: None. L.M. Delhey: None. G.A. Goode: None. A. Beebe: None. E. Børsheim: None. Funding National Institute of General Medical Sciences (P20GM109096)

Redox-Dependent Chromatin Remodeling: A New Function of Nitric Oxide as Architect of Chromatin Structure in Plants

Nitric oxide (NO) is a key signaling molecule in all kingdoms. In plants, NO is involved in the regulation of various processes of growth and development as well as biotic and abiotic stress response. It mainly acts by modifying protein cysteine or tyrosine residues or by interacting with protein bound transition metals. Thereby, the modification of cysteine residues known as protein S-nitrosation is the predominant mechanism for transduction of NO bioactivity. Histone acetylation on N-terminal lysine residues is a very important epigenetic regulatory mechanism. The transfer of acetyl groups from acetyl-coenzyme A on histone lysine residues is catalyzed by histone acetyltransferases. This modification neutralizes the positive charge of the lysine residue and results in a loose structure of the chromatin accessible for the transcriptional machinery. Histone deacetylases, in contrast, remove the acetyl group of histone tails resulting in condensed chromatin with reduced gene expression activity. In plants, the histone acetylation level is regulated by S-nitrosation. NO inhibits HDA complexes resulting in enhanced histone acetylation and promoting a supportive chromatin state for expression of genes. Moreover, methylation of histone tails and DNA are important epigenetic modifications, too. Interestingly, methyltransferases and demethylases are described as targets for redox molecules in several biological systems suggesting that these types of chromatin modifications are also regulated by NO. In this review article, we will focus on redox-regulation of histone acetylation/methylation and DNA methylation in plants, discuss the consequences on the structural level and give an overview where NO can act to modulate chromatin structure.

Covalent Inhibitors of Protein-Protein Interactions Targeting Lysine, Tyrosine, or Histidine Residues.

We have recently reported a series of Lys-covalent agents targeting the BIR3 domain of the X-linked inhibitor of apoptosis protein (XIAP) using a benzamide-sulfonyl fluoride warhead. Using XIAP as a model system, we further investigated a variety of additional warheads that can be easily incorporated into binding peptides and analyzed their ability to form covalent adducts with lysine and other amino acids, including tyrosine, histidine, serine, and threonine, using biochemical and biophysical assays. Moreover, we tested aqueous, plasma stability, cell permeability, and cellular efficacy of the most effective agents. These studies identified aryl-fluoro sulfates as likely the most suitable electrophiles to effectively form covalent adducts with Lys, Tyr, and His residues, given that these agents were cell permeable and stable in aqueous buffer and in plasma. Our studies contain a number of general findings that open new possible avenues for the design of potent covalent protein-protein interaction antagonists.

The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell-cell adhesion.

Cell-cell communication in multicellular organisms depends on the dynamic and reversible phosphorylation of protein tyrosine residues. The receptor-linked protein tyrosine phosphatases (RPTPs) receive cues from the extracellular environment and are well placed to influence cell signaling. However, the direct events downstream of these receptors have been challenging to resolve. We report here that the homophilic receptor PTPRK is stabilized at cell-cell contacts in epithelial cells. By combining interaction studies, quantitative tyrosine phosphoproteomics, proximity labeling and dephosphorylation assays we identify high confidence PTPRK substrates. PTPRK directly and selectively dephosphorylates at least five substrates, including Afadin, PARD3 and δ-catenin family members, which are all important cell-cell adhesion regulators. In line with this, loss of PTPRK phosphatase activity leads to disrupted cell junctions and increased invasive characteristics. Thus, identifying PTPRK substrates provides insight into its downstream signaling and a potential molecular explanation for its proposed tumor suppressor function.

NiII -ATCUN-Catalyzed Tyrosine Nitration in the Presence of Nitrite and Sulfite.

The nitration of tyrosine residues in proteins represents a specific footprint of the formation of reactive nitrogen species (RNS) in vivo. Here, the fusion product of orange protein (ATCUN-ORP) was used as an in vitro model system containing an amino terminal Cu(II)- and Ni(II)-binding motif (ATCUN) tag at the N-terminus and a native tyrosine residue in the metal-cofactor-binding region for the formation of 3-NO2 -Tyr (3-NT). It is shown that NiII -ATCUN unusually performs nitration of tyrosine at physiological pH in the presence of the NO2 - /SO3 2- /O2 system, which is revealed by a characteristic absorbance band at 430 nm in basic medium and 350 nm in acidic medium (fingerprint of 3-NT). Kinetics studies showed that the formation of 3-NT depends on sulfite concentration over nitrite concentration suggesting key intermediate products, identified as oxysulfur radicals, which are detected by spin-trap EPR study by using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). This study describes a new route in the formation of 3-NT, which is proposed to be linked with the sulfur metabolism pathway associated with the progression of disease occurrence in vivo.

Multiple gene silencing in STAT pathway in K562 cells

Context: Chronic myeloid leukemia (CML) is characterized by the presence of a fusion oncoprotein BCR-ABL. This mutation imparts a constitutive phosphorylation activity of tyrosine residues in the cellular proteins. One of the targets of BCR-ABL is the STAT5 protein, which when phosphorylated induces gene expression of antiapoptotic proteins such as BCL-XL. The STAT pathway has been targeted in the past by disrupting any one protein only. A multiple gene silencing has never been done in this pathway. Aim: The aim of this study was to compare the effects of downregulation of BCR-ABL, STAT5A, STAT5B, and BCL-XL, individually and simultaneously, in human CML cell line (K562 cells) through RNA interference (RNAi). Further, gene expression, inhibition of proliferation, and apoptosis induction were assessed in K562 cells. Materials and Methods: K562 cells were transfected with various combinations of small iRNA (siRNA) and the expressions of aforesaid genes were determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. K562 cell proliferation and apoptosis were analyzed using 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide and flow cytometry, respectively. The results were compared through one-way analysis of variance. Results: qPCR and western blotting results post-siRNA transfection confirmed the targeted gene suppression and protein reduction in K562 cells. The cell proliferation assay and apoptosis assay revealed that simultaneous gene silencing of BCR-ABL, STAT5A, STAT5B, and BCL-XL had the highest killing effect on K562 cells as compared to knocking down these genes individually or in any other combinations. Conclusions: This was the first time it was shown that multiple gene silencing in STAT pathway in CML cell line K562 was better as compared to individual gene silencing.