Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B

Protein tyrosine phosphatases regulate signal transduction pathways involving tyrosine phosphorylation and have been implicated in the development of cancer, diabetes, rheumatoid arthritis and hypertension. Increasing evidence suggests that the cellular redox state is involved in regulating tyrosine phosphatase activity through the reversible oxidization of the catalytic cysteine to sulphenic acid (Cys-SOH). But how further oxidation to the irreversible sulphinic (Cys-SO2H) and sulphonic (Cys-SO3H) forms is prevented remains unclear. Here we report the crystal structures of the regulatory sulphenic and irreversible sulphinic and sulphonic acids of protein tyrosine phosphatase 1B (PTP1B), an important enzyme in the negative regulation of the insulin receptor and a therapeutic target in type II diabetes and obesity. We also identify a sulphenyl-amide species that is formed through oxidation of its catalytic cysteine. Formation of the sulphenyl-amide causes large changes in the PTP1B active site, which are reversible by reduction with the cellular reducing agent glutathione. The sulphenyl-amide is a protective intermediate in the oxidative inhibition of PTP1B. In addition, it may facilitate reactivation of PTP1B by biological thiols and signal a unique state of the protein.     

Quantitative reactivity profiling predicts functional cysteines in proteomes

Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.     

Redox regulation of protein tyrosine phosphatase 1B involves a sulphenyl-amide intermediate

The second messenger hydrogen peroxide is required for optimal activation of numerous signal transduction pathways, particularly those mediated by protein tyrosine kinases. One mechanism by which hydrogen peroxide regulates cellular processes is the transient inhibition of protein tyrosine phosphatases through the reversible oxidization of their catalytic cysteine, which suppresses protein dephosphorylation. Here we describe a structural analysis of the redox-dependent regulation of protein tyrosine phosphatase 1B (PTP1B), which is reversibly inhibited by oxidation after cells are stimulated with insulin and epidermal growth factor. The sulphenic acid intermediate produced in response to PTP1B oxidation is rapidly converted into a previously unknown sulphenyl-amide species, in which the sulphur atom of the catalytic cysteine is covalently linked to the main chain nitrogen of an adjacent residue. Oxidation of PTP1B to the sulphenyl-amide form is accompanied by large conformational changes in the catalytic site that inhibit substrate binding. We propose that this unusual protein modification both protects the active-site cysteine residue of PTP1B from irreversible oxidation to sulphonic acid and permits redox regulation of the enzyme by promoting its reversible reduction by thiols.     

一种改进的珙桐(Davidia Involucrata)干种子总RNA提取方法

改进后的方法在提取缓冲液中加入了2％的PVP(分子量10000）和10mM的半胱氨酸以避免多酚类物质的氧化，减少了苯酚抽提的次数。使用该改进的方法可以从平均每克珙桐干种子中获得240μg的总RNA，这些总RNA适合用于体外反转录、Northem杂交以及cDNA文库的构建。     

Identification of the long ubiquitin extension as ribosomal protein S27a

Two proteins of unknown function are encoded by 3' in-frame extensions of ubiquitin genes. The polypeptides are synthesized as an additional 52 or 76-80 amino acids on the C terminus of ubiquitin, an unusual arrangement conserved in man, yeast and plants (J. Callis and R. Vierstra, personal communication). Although not homologous to each other or to ubiquitin, both extension proteins are highly basic and contain patterns of cysteine and histidine similar to those proposed to form 'zinc fingers'. The longer C-terminal extension protein (CEP80) is 30% lysine and arginine and, when denatured, behaves like a small cationic protein. Its properties after isolation in physiological conditions, however, suggested that CEP80 is part of an RNA-protein complex. Using the antibodies that confirmed the presence of CEP80 in eukaryotic cells, we show here that the protein is located on ribosomes. Immunoblotting of rat 40S subunit proteins specifically identifies CEP80 as ribosomal protein S27a.     

暗纹东方纯CD8α基因克隆、原核表达与多克隆抗体制备

CD8是与Ⅰ型主要组织相容性复合体（MHCI）结合,是T细胞表面受体（TCR）的共受体．也是T淋巴细胞表面的重要标志物。该研究报道了暗纹东方纯胸腺等组织中克隆获得CD8αcDNA序列及其相应的基因组序列。克隆到的cDNA序列全长1061bp,包含1个657bp的开放读码框（ORF）,编码218个氨基酸;其对应的基因组序列为1533bp,包含5个内含子和6个外显子。生物信息学分析表明,D8d蛋白质序列由信号肽、胞外可变区、铰链区、跨膜区和胞内区5部分组成。胞外区的可变区和铰链区部分各有两个高度保守的半胱氨酸残基,可能参与链内和链间二硫键的形成。氨基酸序列多重比对表明,暗纹东方鲍与其他鱼类的CD80α,特别是与鲽形目鱼类具有较高的同源性。为进一步研究暗纹东方纯CD8的生物学功能,构建了表达CD8α成熟肽胞外区的重组质粒,诱导表达出重组蛋白。以纯化的重组蛋白为抗原免疫大白兔,制备了抗血清。经间接ELISA法检测抗体效价表明。获得了高效价的特异性暗纹东方纯CD8c~抗体,为进一步研究CD8在鱼类淋巴细胞进化和适应性免疫中的作用奠定了基础。     

Glycoproteins form mixed disulphides with oxidoreductases during folding in living cells

The formation of intra- and interchain disulphide bonds constitutes an integral part of the maturation of most secretory and membrane-bound proteins in the endoplasmic reticulum. Evidence indicates that members of the protein disulphide isomerase (PDI) superfamily are part of the machinery needed for proper oxidation and isomerization of disulphide bonds. Models based on in vitro studies predict that the formation of mixed disulphide bonds between oxidoreductase and substrate is intermediate in the generation of the native intrachain disulphide bond in the substrate polypeptide. Whether this is how thiol oxidoreductases work inside the endoplasmic reticulum is not clear. Nor has it been established which of the many members of the PDI superfamily interacts directly with newly synthesized substrate proteins, because transient mixed disulphides have never been observed in the mammalian endoplasmic reticulum during oxidative protein folding. Here we describe the mechanisms involved in co- and post-translational protein oxidation in vivo. We show that the endoplasmic-reticulum-resident oxidoreductases PDI and ERp57 are directly involved in disulphide oxidation and isomerization, and, together with the lectins calnexin and calreticulin, are central in glycoprotein folding in the endoplasmic reticulum of mammalian cells.     

Nucleotide sequence of epidermal growth factor cDNA predicts a 128,000-molecular weight protein precursor

Epidermal growth factor (EGF) has a profound effect on the differentiation of specific cells in vivo, and has been shown to be a potent mitogenic factor for a variety of cultured cells, of both ectodermal and mesodermal origin (see ref. 1 for review). This 53-amino acid polypeptide of known sequence contains six cysteine residues, which are thought to form three intrachain disulphide bonds. Urogastrone, a polypeptide bearing anti-gastric secretory activity isolated from human urine, which is presumably synthesized in submandibular and Brunner's glands, shares extensive sequence homology (70%) with EGF and may represent the human EGF equivalent. Here we present the sequence of a mouse EGF cDNA clone, which suggests that EGF is synthesized as a large protein precursor of 1,168 amino acids. Our data indicate that the discrepancy between EGF levels in male and female mouse submaxillary glands (MSGs) is due to different EGF mRNA levels in these tissues, and suggest that precursor EGF processing may differ from that described previously for other polypeptide hormones.     

在金刚石膜上电化学氧化对硝基苯酚

利用金刚石膜电极电化学氧化技术可以消除环境污染,该技术可以有效地处理含苯酚、氯酚或其他含酚的化合物以及羧基酸,在大多数的情况下,这些有机物可以被完全矿化.由此表明,电化学氧化技术处理污水中含有苯环的有机物是很有前景的,但相关报道很少.含硝基的有机化合物是工业和农     

季膦盐和钨酸钠催化下双氧水溶液清洁氧化醇和烯烃的研究

首先合成1-羟甲基苯并三唑、1-氯甲基苯并三唑、1,4-二溴丁烷单季膦盐等几种中间体,通过熔点、红外谱图等手段对其进行了结构表征;进而合成1-三苯基膦甲基苯并三唑、双季膦盐和ω-苯并三唑基丁基季膦盐等3种催化剂.其次,对自制的3种催化剂辅助过氧化氢氧化环己醇、苯甲醇、环己烯的性能进行了评价.即利用各季膦盐与钨酸钠构成三种催化体系,在无有机溶剂条件下,实现了30%过氧化氢水溶液清洁催化环己醇、苯甲醇、环己烯为环己酮、苯甲醛(或苯甲酸)、己二酸;考察了3种催化剂分别在3种体系下的催化性能.结果表明:对于环己醇的氧化1-三苯基膦甲基苯并三唑催化剂的效果最好;对于环己烯的氧化仍是1-三苯基膦甲基苯并三唑催化剂的效果最好;对于苯甲醇的氧化ω-苯并三唑基丁基季膦盐的催化效果最好.研究发现:在苯甲醇氧化时,随催化剂种类、体系和过氧化氢加入量的不同,可以选择性地氧化成苯甲醛或苯甲酸.在环己烯氧化时,随催化剂加量、过氧化氢加入量的不同和实验室的条件等的限制选择性很大.     

Cloning and characterization of a gene encoding cysteine proteases from senescent leaves of Gossypium hirsutum

A gene encoding a cysteine proteinase was isolated from senescent leave of cotton (Gossypium hirsutum) cv liaomian No. 9 by utilizing rapid amplification of cDNA end spolymerase chain reaction (RACE-PCR), and a set of consensus oligonucleotide primers was designed to anneal the conserved sequences of plant cysteine protease genes. The cDNA, which designated Ghcysp gene, contained 1368 bp terminating in a poly(A)^ trail, and included a putative 5‘(98 bp) and a 3‘(235 bp) non-coding region. The opening reading frame (ORF) encodes polypeptide 344 amino acids with the predicted molecular mass of 37.88 kD and theoretical pl of 4.80. A comparison of the deduced amino acid sequence with the sequence in the GenBank database has shown considerable sequence similarity to a novel family of plant cysteine proteases. This putative cotton Ghcysp protein shows from 67% to 82% identity to the other plants. All of them share catalytic triad of residues, which are highly conserved in three regions. Hydropaths analysis of the amino acid sequence shows that the Ghcysp is a potential membrane protein and localizes to the vacuole, which has a transmembrane helix between resides 7-25. A characteristic feature of Ghcysp is the presence of a putative vacuole-targeting signal peptide of 19-amino acid residues at the N-terminal region. The expression of Ghcysp gene was determined using northern blot analysis. The Ghcysp mRNA levels are high in development senescent leaf but below the limit of detection in senescent root, hypocotyl, faded flower, 6 d post anthesis ovule, and young leaf.     

嗜热真菌Thermomyces langinosus编码丝/苏氨酸蛋白激酶部分cDNA的克隆及序列分析

根据几种丝状真菌保守的氨基酸序列,设计了一组简并性的引物,从嗜热真菌Thermomyceslanginosus中提取总RNA,利用RT-PCR的方法,我们得到了一个1243bp的cDNA的片段。片段回收纯化后连接到pGEM-Teasy载体上,PCR扩增重组质粒证实这个长约1200bp片段已经插到载体上。序列分析发现和裂殖酵母的蛋白激酶dis1非常相似,比较两者3'氨基酸序列发现同源性达28%以上。其推断的氨基酸序列上包含有6个丝/苏氨酸蛋白激酶的保守亚区。这些都表明它编码的基因可能是一个新的丝/苏氨酸蛋白激酶。     

Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase

The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.     

Epidermal growth factor receptor occupancy inhibits vaccinia virus infection

Vaccinia virus encodes VGF, an early protein of relative molecular mass 19,000 (19K) which, from amino-acid residues 45 to 85, is homologous in 19 residues to epidermal growth factor (EGF), and transforming growth factor-alpha (TGF-alpha). The conserved sequence includes a region of high homology (6 out of 10 amino acids) from residues 71 to 80, corresponding to the third disulphide loop of both EGF and TGF-alpha. This region has recently been shown to contain a binding region of TGF-alpha for the EGF receptor, and this raises the question of whether vaccinia virus utilizes the EGF receptor in order to bind to and infect cells. We now show that occupancy of the EGF receptor inhibits vaccinia virus infection. Inhibition is observed in a dose-dependent fashion by pre-treatment with either EGF or synthetic decapeptide antagonists of EGF's mitogenic activity which correspond to the sequence of the third disulphide loop of VGF or TGF-alpha. The relative ability of the peptides to inhibit vaccinia virus infection parallels their binding affinity to the EGF receptor.     

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

Two large-scale yeast two-hybrid screens were undertaken to identify protein-protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. In one approach, we constructed a protein array of about 6,000 yeast transformants, with each transformant expressing one of the open reading frames as a fusion to an activation domain. This array was screened by a simple and automated procedure for 192 yeast proteins, with positive responses identified by their positions in the array. In a second approach, we pooled cells expressing one of about 6,000 activation domain fusions to generate a library. We used a high-throughput screening procedure to screen nearly all of the 6,000 predicted yeast proteins, expressed as Gal4 DNA-binding domain fusion proteins, against the library, and characterized positives by sequence analysis. These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. These data reveal interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes. The results of these screens are shown here.     

Proton translocation by cytochrome c oxidase.

Cell respiration in mitochondria and some bacteria is catalysed by cytochrome c oxidase, which reduces O2 to water, coupled with translocation of four protons across the mitochondrial or bacterial membrane. The enzyme's catalytic cycle consists of a reductive phase, in which the oxidized enzyme receives electrons from cytochrome c, and an oxidative phase, in which the reduced enzyme is oxidized by O2. Previous studies indicated that proton translocation is coupled energetically only to the oxidative phase, but this has been challenged. Here, with the purified enzyme inlaid in liposomes, we report time-resolved measurements of membrane potential, which show that half of the electrical charges due to proton-pumping actually cross the membrane during reduction after a preceding oxidative phase. pH measurements confirm that proton translocation also occurs during reduction, but only when immediately preceded by an oxidative phase. We conclude that all the energy for proton translocation is conserved in the enzyme during its oxidation by O2. One half of it is utilized for proton-pumping during oxidation, but the other half is unlatched for this purpose only during re-reduction of the enzyme.     

The yeast ubiquitin gene: head-to-tail repeats encoding a polyubiquitin precursor protein

Ubiquitin, a 76-residue protein, occurs in cells either free or covalently joined to a variety of protein species, from chromosomal histones to cytoplasmic proteins. Conjugation of ubiquitin to proteolytic substrates is essential for the selective degradation of intracellular proteins in higher eukaryotes. We show here that a protein homologous to human ubiquitin exists in the yeast Saccharomyces cerevisiae, and that yeast extracts conjugate human ubiquitin to a variety of endogenous proteins in an ATP-dependent reaction. We have isolated the S. cerevisiae ubiquitin gene and found it to contain six consecutive ubiquitin-coding repeats in a found it to contain six consecutive ubiquitin-coding repeats in a head-to-tail arrangement. This apparently unique gene organization suggests that yeast ubiquitin is generated by processing of a precursor protein in which several exact repeats of the ubiquitin amino acid sequence are joined directly via Gly-Met peptide bonds between the last and first residues of mature ubiquitin, respectively. Ubiquitin-coding yeast DNA repeats are restricted to a single genomic locus; although the sequenced repeats differ in up to 27 of 228 bases per repeat, they encode identical amino acid sequences. As this predicted amino acid sequence differs in only 3 of 76 residues from that of ubiquitin in higher eukaryotes, ubiquitin is apparently the most conserved of known proteins.     

Leptin stimulates fatty-acid oxidation by activating AMP-activated protein kinase.

Leptin is a hormone secreted by adipocytes that plays a pivotal role in regulating food intake, energy expenditure and neuroendocrine function. Leptin stimulates the oxidation of fatty acids and the uptake of glucose, and prevents the accumulation of lipids in nonadipose tissues, which can lead to functional impairments known as "lipotoxicity". The signalling pathways that mediate the metabolic effects of leptin remain undefined. The 5'-AMP-activated protein kinase (AMPK) potently stimulates fatty-acid oxidation in muscle by inhibiting the activity of acetyl coenzyme A carboxylase (ACC). AMPK is a heterotrimeric enzyme that is conserved from yeast to humans and functions as a 'fuel gauge' to monitor the status of cellular energy. Here we show that leptin selectively stimulates phosphorylation and activation of the alpha2 catalytic subunit of AMPK (alpha2 AMPK) in skeletal muscle, thus establishing a previously unknown signalling pathway for leptin. Early activation of AMPK occurs by leptin acting directly on muscle, whereas later activation depends on leptin functioning through the hypothalamic-sympathetic nervous system axis. In parallel with its activation of AMPK, leptin suppresses the activity of ACC, thereby stimulating the oxidation of fatty acids in muscle. Blocking AMPK activation inhibits the phosphorylation of ACC stimulated by leptin. Our data identify AMPK as a principal mediator of the effects of leptin on fatty-acid metabolism in muscle.