Revealing the functional roles of tyrosine sulfation using synthetic sulfopeptides and sulfoproteins

The decoration of proteins with post-translational modifications (PTMs) serves as a mechanism to expand the functional repertoire of the proteome. Tyrosine sulfation is a PTM that has been shown to be a key regulator of extracellular protein–protein interactions in a select number of examples. However, the challenges associated with identifying and characterising the functional consequences of tyrosine sulfation have hindered our ability to understand the full scope of its role in the wider proteome when compared with that of other PTMs, for example, phosphorylation and glycosylation. In this account, we highlight recent advances in the prediction and detection of tyrosine sulfation and outline the need for continued innovation in this area. We also discuss the utility of emerging solid-phase synthesis and peptide ligation strategies for accessing libraries of homogeneously sulfated peptides and proteins to help reveal functional aspects of the sulfoproteome.     

Phosphorylation and consequent stimulation of the tyrosine kinase c-Abl by PKA in mouse spermatozoa; its implications during capacitation

Upon ejaculation, spermatozoa undergo a series of post-translational modifications in a process known as capacitation in order to prepare for fertilization. In the absence of capacitation, fertilization cannot occur. Spermatozoa are unusual in that one of the hallmarks of capacitation is a global up-regulation in phosphotyrosine expression, which is known to be mediated upstream by PKA. Little is known about the signaling events downstream of PKA apart from the involvement of SRC, as a key mediator of PKA-induced tyrosine phosphorylation in the sperm tail. Here we describe the presence of c-Abl in mouse spermatozoa. In vitro analysis confirmed that PKA can up-regulate c-Abl kinase activity. In vivo, this tyrosine kinase was found to associate, and become threonine phosphorylated by PKA in the sperm flagellum. By treating spermatozoa with hemolysin we could demonstrate that a significant proportion of the tyrosine phosphorylation associated with capacitation could be suppressed by the c-Abl inhibitor, Gleevac. This is the first report of c-Abl being up-regulated by PKA for any cell type. We present a model, whereby these kinases may operate together with SRC to ensure optimal levels of tyrosine phosphorylation in the sperm flagellum during the attainment of a capacitated state.     

Analysis of sequence requirements for protein tyrosine sulfation.

We analyzed sequences surrounding known tyrosine sulfation sites to determine the characteristics that distinguish these sites from those that do not undergo sulfation. Tests evaluated the number and position of acidic, basic, hydrophobic, and small amino acids, as well as disulfide and N-glycosylation (sugar) sites. We determined that composition-based tests that select close to 100% of known tyrosine sulfation sites reject 97% of the non-sulfated tyrosines. The acidic test, by far the most selective, eliminated 95% of the non-sulfated tyrosine residues and none of the sulfated tyrosines. Including the basic, hydrophobic, and disulfide tests increased the elimination rate to 97%. Whereas no position flanking the tyrosine residues had the same amino acid always present, imperfectly conserved amino acids found in some positions will improve the specificity of the tests.     

Aldimine to ketoamine isomerization (Amadori rearrangement) potential at the individual nonenzymic glycation sites of hemoglobin a: Preferential inhibition of glycation by nucleophiles at sites of low isomerization potential

The relative roles of the two structural aspects of nonenzymic glycation sites of hemoglobin A, namely the ease with which the amino groups could form the aldimine adducts and the propensity of the microenvironments of the respective aldimines to facilitate the Amadori rearrangement, in dictating the site selectivity of nonenzymic glycation with aldotriose has been investigated. The chemical reactivity of the amino groups of hemoglobin A forin vitro reductive glycation with aldotriose is distinct from that in the nonreductive mode. The reactivity of amino groups of hemoglobin A toward reductive glycation (i.e., propensity for aldimine formation) decreases in the order Val-1(), Val-1(), Lys-66(), Lys-61(), and Lys-16(). The overall reactivity of hemoglobin A toward nonreductive glycation decreased in the order Lys-16(), Val-1(), Lys-66(), Lys-82(), Lys-61(), and Val-1(). Since the aldimine is the common intermediate for both the reductive and nonreductive modification, the differential selectivity of protein for the two modes of glycation is clearly a reflection of the propensity of the microenvironments of nonenzymic glycation sites to facilitate the isomerization reaction (i.e., Amadori rearrangement). A semiquantitative estimate of this propensity of the microenvironment of the nonenzymic glycation sites has been obtained by comparing the nonreductive (nonenzymic) and reductive modification at individual glycation sites. The microenvironment of Lys-16() is very efficient in facilitating the rearrangement and the relative efficiency decreases in the order Lys-16(), Lys-82(), Lys-66(), Lys-61(), Val-1(), and Val-1(). The propensity of the microenvironment of Lys-16() to facilitate the Amadori rearrangement of the aldimine is about three orders of magnitude higher than that of Val-1() and is about 50 times higher than that of Val-1(). The extent of nonenzymic glycation at the individual sites is modulated by various factors, such as thepH, concentration of aldotriose, and the concentration of the protein. The nucleophiles—such as tris, glycine ethyl ester, and amino guanidine—inhibit the glycation by trapping the aldotriose. The nonenzymic glycation inhibitory power of nucleophile is directly related to its propensity to form aldimine. Thus, the extent of inhibition of nonenzymic glycation at a given site by a nucleophile directly reflects the relative role ofpK _a of the site in dictating the glycation at that site. The nonenzymic glycation of an amino group of a protein is an additive/synergestic consequence of the propensity of the site to form aldimine adducts on one hand, and the propensity of its microenvironment to facilitate the isomerization of the aldimines to ketoamines on the other. The isomerization potential of microenvironment plays the dominant role in dictating the site specificity of the nonenzymic glycation of proteins.     

Stereoselective and manganese-dependent sulfation and urinary excretion of -form and -form meta-tyrosine O-sulfate by Sprague–Dawley rats

In our previous studies, we have demonstrated the stereoselective and manganese-dependent sulfation of tyrosine and Dopa isomers by human monoamine (M)-form phenol sulfotransferase (PST). In the present study, we investigated the occurrence of these phenomena in vivo using Sprague–Dawley rats as an experimental model. Three groups of six male rats were orally introduced with 1 ml of, respectively, 3 mM, 10 mM and 30 mM MnCl₂ with a constant level of 0.2 mM -m-tyrosine per day for 7 days. Their urine was collected and analyzed for the presence of sulfated -m-tyrosine ( -m-TyrS) by ion-pair HPLC using a C18 reversed-phase column. The level of urinary -m-TyrS, which was detected in the urine of the MnCl₂-treated rats but not control rats, appeared to increase proportionally to the amount of MnCl₂ administered. Chiral HPLC was employed to differentiate the -form and -form m-TyrS present in the urine sample of MnCl₂-treated rats. Both -m-TyrS and -m-TyrS were detected, with the -form being present at significantly higher level than the -form.     

Novel tyrosine phosphorylation sites in rat skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS

Tyrosine phosphorylation plays a fundamental role in many cellular processes including differentiation, growth and insulin signaling. In insulin resistant muscle, aberrant tyrosine phosphorylation of several proteins has been detected. However, due to the low abundance of tyrosine phosphorylation (<1% of total protein phosphorylation), only a few tyrosine phosphorylation sites have been identified in mammalian skeletal muscle to date. Here, we used immunoprecipitation of phosphotyrosine peptides prior to HPLC-ESI-MS/MS analysis to improve the discovery of tyrosine phosphorylation in relatively small skeletal muscle biopsies from rats. This resulted in the identification of 87 distinctly localized tyrosine phosphorylation sites in 46 muscle proteins. Among them, 31 appear to be novel. The tyrosine phosphorylated proteins included major enzymes in the glycolytic pathway and glycogen metabolism, sarcomeric proteins, and proteins involved in Ca(2+) homeostasis and phosphocreatine resynthesis. Among proteins regulated by insulin, we found tyrosine phosphorylation sites in glycogen synthase, and two of its inhibitors, GSK-3α and DYRK1A. Moreover, tyrosine phosphorylation sites were identified in several MAP kinases and a protein tyrosine phosphatase, SHPTP2. These results provide the largest catalogue of mammalian skeletal muscle tyrosine phosphorylation sites to date and provide novel targets for the investigation of human skeletal muscle phosphoproteins in various disease states.     

Entry of animal viruses and macromolecules into cells

The entry of animal viruses into cells is mediated by conformational changes in certain virion-particle components. These changes are triggered by the binding of virions to receptors and are influenced by low pH during receptor-mediated endocytosis. These conformational alterations promote the interaction of some viral proteins with cellular membranes thereby leading to transient pore formation and the disruption of ionic and pH gradients. The entry of toxins that do not possess receptors on the cell surface is promoted during the translocation of the virus genome or the nucleocapsid to the cytoplasm. A model is now presented which indicates that efficient virus translocation through cellular membranes requires energy, that may be generated by a protonmotive force. The entry of some animal viruses, as promoted by low pH, should thus only take place when a pH gradient and/or a membrane potential exist, but will not take place if these are dissipated, even if virion particles are present in an acidic enviroment.     

Prediction of mutation trend in hemagglutinins and neuraminidases from influenza A viruses by means of cross-impact analysis

In this study, we use the cross-impact analysis to define the relationship among impact, mutation, and outbreak of bird flu. Then we use the distribution rank, which is developed by us over last several years, to quantify the mutations from amino acid sequences of 134 hemagglutinins and 97 neuraminidases. With the help of Bayesian equation, we calculate the probability of occurring of mutation in H5, H6, and H9 hemagglutinins, and N1 and N2 neuraminidases. Finally, we estimate the probability of occurring of mutation with different intensities of an impact. Although we have no means to predict an impact, which is severe enough to lead to the mutations in hemagglutinins and neuraminidases resulting in the outbreak of bird flu, we can in principle monitor the changes in distribution rank along the time course, and predict the trend of mutations, even to predict the degree of outbreak of bird flu.     

2015-2020年大连市流感病毒分离鉴定情况分析

对2015-2020年大连市流感病毒分离鉴定情况进行对比分析, 为大连市流感防控工作提供参考。

采集大连市2家国家级流感监测哨点医院的流感样病例咽拭子样本, 用MDCK细胞和鸡胚分别进行病毒分离培养, 并采用HA试验和HI试验对分离的病毒滴度和型别进行鉴定。

2015-2020年共分离培养流感病毒核酸检测阳性的咽拭子1 055份, 其中MDCK细胞分离出流感病毒501株, 鸡胚分离出流感病毒72株, 总体病毒分离率54.31%。MDCK细胞分离出A(H1N1)、A(H3N2)、B(Victoria)和B(Yamagata)型病毒, 鸡胚对A(H3N2)型病毒不敏感, 但可以分离出A(H1N1)、B(Victoria)和B(Yamagata)型病毒。每年的优势毒株虽不同, 但分离流感病毒的月份均在流行季内, 与北方流行形势一致。

MDCK细胞与鸡胚的流感病毒分离率不同。大连市每年流感流行的优势株和流行程度虽不同, 但流行程度处于相对平稳状态。

     

Identification of four sites of stimulated tyrosine phosphorylation in the MUC1 cytoplasmic tail

MUC1 is an integral membrane protein expressed on the apical surface of epithelial cells where it acts as a signaling receptor. Its cytoplasmic tail (CT) contains seven, highly conserved tyrosine residues, some of which are constitutively phosphorylated and serve as recognition sites for SH2 domain proteins involved in intracellular signal transduction. However, no studies have determined which MUC1 tyrosines are phosphorylated or which signaling pathways are activated in response to stimulation of its ectodomain. In this report, we used our previously characterized CD8/MUC1 chimeric protein that is tyrosine phosphorylated on the MUC1 CT in response to extracellular treatment with CD8 antibody and performed site-directed mutagenesis of all seven tyrosines, both individually and in multiple combinations, to identify the particular sites of stimulated phosphorylation. We observed four phosphorylation sites, three present in sequence motifs with known signaling potential (Y(20), Y(46), and Y(60)) and one previously uncharacterized (Y(29)). These results are discussed in the context of the role of MUC1 in signal transduction.     

Labeling of v-Src and BCR-ABL tyrosine kinases with [C]herbimycin A and its use in the elucidation of the kinase inactivation mechanism

The ansamycin antibiotic, herbimycin A, selectively inactivates cytoplasmic tyrosine kinases, most likely by binding irreversibly to the reactive SH group(s) of kinases. To further investigate the mechanism of herbimycin A action, we attempted to label tyrosine kinases with [¹⁴C]herbimycin A. p60^v-src and p2 10^BCR-ABL in immune complexes were labeled with [¹⁴C]herbimycin A, demonstrating that the antibiotic binds directly to tyrosine kinases. Digestion of [¹⁴C]herbimycin A-labeled p60^v-src with Staphylococcus taureus V8 protease revealed that the herbimycin A binding site is within the C-terminal 26-kDa fragment of p60^v-src, which contains the tyrosine kinase domain. Herbimycin A treatment inhibited labeling of p60^v-src by [¹⁴]C]fluorosulfonylbenzoyl adenosine, an affinity labeling reagent of nucleotide binding sites, indicating that herbimycin A-modified p60^v-src cannot interact with ATP. The results suggest that herbimycin A inactivates tyrosine kinases by binding directly to the kinase domain, thereby inhibiting access to ATP.     

Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus

On 15 April and 17 April 2009, novel swineorigin influenza A (H1N1) virus was identifi ed in specimens obtained from two epidemiologically unlinked patients in the United States. The ongoing outbreak of novel H1N1 2009 influenza (swine influenza) has caused more than 3,99,232 laboratory confi rmed cases of pandemic influenza H1N1 and over 4735 deaths globally. This novel 2009 influenza virus designated as H1N1 A/swine/California/04/2009 virus is not zoonotic swine flu and is transmitted from person to person and has higher transmissibility then that of seasonal influenza viruses. In India the novel H1N1 virus infection has been reported from all over the country. A total of 68,919 samples from clinically suspected persons have been tested for influenza A H1N1 across the country and 13,330 (18.9%) of them have been found positive with 427 deaths. At the All India Institute of Medical Sciences, New Delhi India, we tested 1096 clinical samples for the presence of novel H1N1 influenza virus and seasonal influenza viruses. Of these 1096 samples, 194 samples (17.7%) were positive for novel H1N1 influenza virus and 197 samples (18%) were positive for seasonal influenza viruses. During outbreaks of emerging infectious diseases accurate and rapid diagnosis is critical for minimizing further spread through timely implementation of appropriate vaccines and antiviral treatment. Since the symptoms of novel H1N1 influenza infection are not specifi c, laboratory confi rmation of suspected cases is of prime importance.     

Identification of the insulin-responsive tyrosine phosphorylation sites on IRSp53

The 53-kDa insulin receptor substrate protein (IRSp53) is part of a regulatory network that organises the actin cytoskeleton in response to stimulation by small GTPases, promoting formation of actin-rich cell protrusions such as filopodia and lamellipodia. It had been established earlier that IRSp53 is tyrosine phosphorylated in response to stimulation of the insulin and insulin-related growth factor receptors, but the consequences of tyrosine phosphorylation for IRSp53 function are unknown. Here, we have used a variety of IRSp53 truncation and point mutants to identify insulin-responsive tyrosine phosphorylation sites on IRSp53. We have found that the C-terminal half of IRSp53 (residues 251-521) undergoes tyrosine phosphorylation in response to insulin stimulation of the insulin beta receptor or epidermal growth factor stimulation via the epidermal growth factor receptor, and that the key residue for insulin receptor-mediated phosphorylation is tyrosine 310, located in a region between the N-terminal IRSp53/MIM homology domain (IMD, residue 1-250) and the central SH3 domain (residues 374-438) that is predicted to be natively unstructured. Mutation of tyrosine 310 to phenylalanine or glutamic acid abrogates the phosphorylation in response to insulin stimulation, but not in response to stimulation of the epidermal growth factor receptor. The N-terminal IMD, which mediates dimerisation of IRSp53, is required for efficient tyrosine phosphorylation downstream of either the insulin or epidermal growth factor receptor stimulation, yet does not appear to include a tyrosine-phosphorylated site itself. Thus, we have identified tyrosine 310 as a primary site of tyrosine phosphorylation in response to insulin signalling and we have shown that although IRSp53 is tyrosine phosphorylated in response to epidermal growth factor receptor signalling, tyrosine 310 is not crucial. Furthermore, the tyrosine phosphorylation status does not appear to affect the cell morphology and production of filopod-like structures upon expression of IRSp53.     

Characterization of a novel modification of a CHO-produced mAb: Evidence for the presence of tyrosine sulfation

Herein we describe the investigation of a Chinese hamster ovary (CHO)-expressed human mAb molecule found partially modified by a +80 Da adduct. This mass difference, suggestive of a single sulfation or phosphorylation addition, was observed by mass analysis of the intact and reduced molecule by mass spectrometry (MS). The modification was located on tyrosine 31 (Y31) of the light chain in the complementarity-determining region 1 by liquid chromatography (LC)-MS peptide mapping and electron transfer dissociation fragmentation. The complete loss of the 80 Da modification moiety during collision induced dissociation fragmentation suggested this modification could not be a tyrosine phosphorylation. Treatment of the mAb with alkaline phosphatase confirmed our hypothesis. Western blot experiment using anti-tyrosine sulfation antibody and LC retention time correlation with corresponding synthetic sulfated peptides further confirmed the identification of tyrosine sulfation on the light chain. The unique sequence motif with neighboring acidic amino acids and local secondary structure might play a role to make Y31 a substrate residue for sulfation. This type of modification, to our knowledge, has not been previously reported for CHO-produced human IgG antibodies.     

The role of tyrosine sulfation in the dimerization of the CXCR4:SDF‐1 complex

Oligomerization of G protein‐coupled receptors is a recognized mode of regulation of receptor activities, with alternate oligomeric states resulting in different signaling functions. The CXCR4 chemokine receptor is a G protein‐coupled receptor that is post‐translationally modified by tyrosine sulfation at three sites on its N‐terminus (Y7, Y12, Y21), leading to enhanced affinity for its ligand, stromal cell derived factor (SDF‐1, also called CXCL12). The complex has been implicated in cancer metastasis and is a therapeutic target in cancer treatment. Using molecular dynamics simulation of NMR‐derived structures of the CXCR4 N‐terminus in complex with SDF‐1, and calculations of electrostatic binding energies for these complexes, we address the role of tyrosine sulfation in this complex. Our results show that sulfation stabilizes the dimeric state of the CXCR4:SDF‐1 complex through hydrogen bonding across the dimer interface, conformational changes in residues at the dimer interface, and an enhancement in electrostatic binding energies associated with dimerization. These findings suggest a mechanism through which post‐translational modifications such as tyrosine sulfation might regulate downstream function through modulation of the oligomeric state of the modified system.     

Introduction of N-linked glycans in the lectin domain of surfactant protein D: impact on interactions with influenza A viruses

Porcine surfactant protein D (pSP-D) displays distinctively strong, broad-range inhibitory activity against influenza A virus (IAV). N-Linked glycosylation of the carbohydrate recognition domain (CRD) of pSP-D contributes to the high affinity of this collectin for IAV. To investigate the role of the N-linked glycan further, HEK293E protein expression was used to produce recombinant pSP-D (RpSP-D) that has similar structural and antiviral properties as NpSP-D. We introduced an additional N-linked glycan in the CRD of RpSP-D but this modification did not alter the antiviral activity. Human SP-D is unglycosylated in its CRD and less active against IAV compared with pSP-D. In an attempt to modify its antiviral properties, several recombinant human SP-D (RhSP-D) mutants were constructed with N-linked glycans introduced at various locations within its CRD. To retain lectin activity, necessary for the primary interactions between SP-D and IAV, N-linked glycosylation of RhSP-D was shown to be restricted to the corresponding position in the CRD of either pSP-D or surfactant protein A (SP-A). These N-glycosylated RhSP-D mutants, however, did not show increased neutralization activity against IAV. By developing RhSP-D mutants that also have the pSP-D-specific Ser-Gly-Ala loop inserted in the CRD, we could demonstrate that the N-linked glycan-mediated interactions between pSP-D and IAV involves additional structural prerequisites of the pSP-D CRD. Ultimately, these studies will help to develop highly effective SP-D-based therapeutic and prophylactic drugs against IAV.     

Fate of 130 hemagglutinins from different influenza A viruses

In this study, we use our probabilistic models to analyze 130 hemagglutinins from different influenza A virus in order to gain the insight into their fate. The results provide three lines of evidence regarding the H5, H6, and H9 hemagglutinins: (i) the H5 hemagglutinins are more sensitive to mutations, this is the current state of the H5, H6, and H9 hemagglutinins; (ii) the H5 hemagglutinins had experienced more mutations in the past, this is the history of the H5, H6, and H9 hemagglutinins; and (iii) the H6 hemagglutinins has a bigger potential towards future mutations, this is the future of the H5, H6, and H9 hemagglutinins. Furthermore, this study gives two clues on the mutation tendency that is a degeneration process and the species susceptibility that is the chickens and ducks.     

Enhanced phosphorylation and enzymatic activity of phosphoglucomutase by the Btk29A tyrosine kinase in Drosophila

The Drosophila Btk29A tyrosine kinase is suggested to be involved in diverse processes, although its target proteins are unknown. In the present study, we investigated substrates of Btk29A tyrosine kinase by expressing a catalytically activated form of Btk29A-P1 (Btk-EG) in Drosophila compound eyes. Expression in eye disks led to the development of the rough-eye phenotype and increased tyrosine phosphorylation of a 65-kDa protein. Partial amino acid sequence analysis of this protein showed that it was phosphoglucomutase. Phosphoglucomutase activity in heads from Btk-EG-expressing flies was higher than that in controls, suggesting that the levels of tyrosine phosphorylation and activity of the enzyme are associated with Btk29A tyrosine kinase activity.