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.     

Preferential relaxation of supercoiled DNA containing a hexadecameric recognition sequence for topoisomerase I

In prokaryotes, the degree of supercoiling of DNA can profoundly influence the use of specific promoters. In eukaryotes, a variety of indirect observations suggest that DNA topology has a similar importance in proper gene expression. Much attention has therefore been focused on the cellular proteins that control DNA supercoiling, among which are the enzymes topoisomerase I and II. A hexadecameric sequence functions as a strong attraction site for topoisomerase I. Here we report that the interaction of topoisomerase I with this sequence motif is highly specific, because a single base-pair substitution prevents strand cleavage and thereby catalytic activity at the sequence. Thus, supercoiled DNA containing the recognition sequence is relaxed preferentially by topoisomerase I compared to a control, but no difference in the relaxation rate is observed for supercoiled DNA carrying the mutated sequence. The preference for the recognition sequence seems to be an intrinsic property of all eukaryotic type I topoisomerases, suggesting that the interaction might be important in a fundamental biological process.     

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.     

准噶尔盆地车排子地区新近系沙湾组层序地层格架分析

 根据陆相地层层序在地震剖面和电测曲线上的识别标志、合成记录标志以及岩石类型组合特点等方面的特征,将车排子地区新近系沙湾组划分出1个二级层序和2个三级层序。其中,层序I为辫状河三角洲层序,层序II为湖泊层序。又可以根据各层序的特点,将其分为3个体系域：低水位体系域、湖侵体系域和高水位体系域。针对研究区目的层段层序发育的特点,在层序地层单元划分和对比的基础上,结合构造背景和地层厚度的变化,展示了该区层序东南部厚度较大,发育完整,厚度稳定;西北部由于遭受剥蚀,厚度较小,层序发育不完整的格架特征。初步分析了层序与含油气性的关系,预测了不同层序的勘探重点和目标,认为层序I的低水位体系域和层序II的湖侵体系域为寻找岩性油气藏的有利部位。     

Structural basis of protein phosphatase 1 regulation

The coordinated and reciprocal action of serine/threonine (Ser/Thr) protein kinases and phosphatases produces transient phosphorylation, a fundamental regulatory mechanism for many biological processes. The human genome encodes a far greater number of Ser/Thr protein kinases than of phosphatases. Protein phosphatase 1 (PP1), in particular, is ubiquitously distributed and regulates a broad range of cellular functions, including glycogen metabolism, cell-cycle progression and muscle relaxation. PP1 has evolved effective catalytic machinery but lacks substrate specificity. Substrate specificity is conferred upon PP1 through interactions with a large number of regulatory subunits. The regulatory subunits are generally unrelated, but most possess the RVxF motif, a canonical PP1-binding sequence. Here we reveal the crystal structure at 2.7 A resolution of the complex between PP1 and a 34-kDa N-terminal domain of the myosin phosphatase targeting subunit MYPT1. MYPT1 is the protein that regulates PP1 function in smooth muscle relaxation. Structural elements amino- and carboxy-terminal to the RVxF motif of MYPT1 are positioned in a way that leads to a pronounced reshaping of the catalytic cleft of PP1, contributing to the increased myosin specificity of this complex. The structure has general implications for the control of PP1 activity by other regulatory subunits.     

A protein-tyrosine phosphatase with sequence similarity to the SH2 domain of the protein-tyrosine kinases.

The phosphorylation of proteins at tyrosine residues is critical in cellular signal transduction, neoplastic transformation and control of the mitotic cycle. These mechanisms are regulated by the activities of both protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPases). As in the PTKs, there are two classes of PTPases: membrane associated, receptor-like enzymes and soluble proteins. Here we report the isolation of a complementary DNA clone encoding a new form of soluble PTPase, PTP1C. The enzyme possesses a large noncatalytic region at the N terminus which unexpectedly contains two adjacent copies of the Src homology region 2 (the SH2 domain) found in various nonreceptor PTKs and other cytoplasmic signalling proteins. As with other SH2 sequences, the SH2 domains of PTP1C formed high-affinity complexes with the activated epidermal growth factor receptor and other phosphotyrosine-containing proteins. These results suggest that the SH2 regions in PTP1C may interact with other cellular components to modulate its own phosphatase activity against interacting substrates. PTPase activity may thus directly link growth factor receptors and other signalling proteins through protein-tyrosine phosphorylation.     

Fibonacci数和Lucas数的几个性质

通过对Ｆｉｂｏｎａｃｃｉ数列和Ｌｕｃａｓ数列的研究，利用组合方法推出两数列的几个性质。     

计算机辅助的豆壳过氧化物酶分子序列分析

从生物信息学角度 ,利用生物大分子数据库 (GENEBANK、SWISS PROT和PDB)及软件技术 (DNASIS和PROSIS)对豆壳过氧化物酶分子进行了序列分析及结构预测 ;通过与其它植物及真菌来源的过氧化物酶的比较研究 ,分析了结构保守性与功能域的关系 ,从分子水平探讨了植物过氧化物酶超家族的活性位点局部保守序列、折叠模式及序列结构域特征 .     

四川资阳及邻区震旦系灯影组储层段沉积及层序地层学特征

资阳地区灯影组储层段为一套受波浪作用为主的浅水台坪白云岩沉积,由17种岩石微相和5种相序组成的地层中米级—亚米级沉积旋回明显。其储层段由三个不完整的层序构成,高水位体系域沉积构成了层序的主体,层序界面为I型和Ⅱ型。沉积和层序特征受到海平面变化、构造沉降和碳酸盐沉积速度的共同控制。     

Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size.

Peptides bound to class I molecules are 8-10 amino acids long, and possess a binding motif representative of peptides that bind to a given class I allele. In the only published study of naturally processed peptides bound to class II molecules (mouse I-Ab and I-Eb), these peptides were longer (13-17 amino acids) and had heterogenous carboxy terminals but precise amino-terminal truncations. Here we report the characterization of acid-eluted peptides bound to HLA-DR1 by high-performance liquid chromatography, mass spectrometry and microsequencing analyses. The relative molecular masses of the peptides varied between 1,602 and 2,996 (13-25 residues), the most abundant individual M(r) values being between 1,700 and 1,800, corresponding to an average peptide length of 15 residues. Complete sequence data were obtained for twenty peptides derived from five epitopes, of which all but one were from self proteins. These peptides represented sets nested at both the N- and C-terminal ends. Binding experiments confirmed that all of the isolated peptides had high affinity for the groove of DR1. Alignment of the peptides bound to HLA-DR1 and the sequences of 35 known HLA-DR1-binding peptides revealed a putative motif. Although peptides bound to class II molecules may have some related features (due to the nonpolymorphic HLA-DR alpha-chain), accounting for degenerate binding to different alleles, particular amino acids in the HLA-DR beta-chains presumably define allelic specificity of peptide binding.     

含RGD序列水蛭素嵌合抗栓剂的构建与表达

通过对水蛭素及一些含有精氨酸-甘氨酸-天冬氨酸(RGD)序列的多肽类血小板聚集抑制剂结构与功能的分析,设计并构建了两个在水蛭素C端融合RGD序列的嵌合分子。嵌合体基因分别重组到表达载体pET-21a(+)中并转化大肠杆菌BL21(DE3)。经限制酶消化和DNA序列分析,证明两种重组质粒与设计完全一致。由于RGD-水蛭素嵌合基因上游连接了金黄色葡萄球菌蛋白A(SPA)的信号肽序列,在IPTG诱导下两种嵌合分子都获得了分泌表达,表达产物主要集中在细胞周质空间。通过离子交换层析和凝胶过滤层分别对两种嵌合体蛋白进行纯化,纯化产物在Tricine-SDS-PAGE中都显示为单一条带。活性分析结果表明两种嵌合体蛋白在保留水蛭素抗凝血酶活力的同时,还呈现抗血小板聚集活性。     

Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

The aminoacyl-transfer RNA synthetases (aaRS) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology. Out of the 18 known aaRS, only 9 referred to as class I synthetases (GlnRS, TyrRS, MetRS, GluRS, ArgRS, ValRS, IleRS, LeuRS, TrpRS), display two short common consensus sequences ('HIGH' and 'KMSKS') which indicate, as observed in three crystal structures, the presence of a structural domain (the Rossman fold) that binds ATP. We report here the sequence of Escherichia coli ProRS, a dimer of relative molecular mass 127,402, which is homologous to both ThrRS and SerRS. These three latter aaRS share three new sequence motifs with AspRS, AsnRS, LysRS, HisRS and the beta subunit of PheRS. These three motifs (motifs 1, 2 and 3), in a search through the entire data bank, proved to be specific for this set of aaRS (referred to as class II). Class II may also contain AlaRS and GlyRS, because these sequences have a typical motif 3. Surprisingly, this partition of aaRS in two classes is found to be strongly correlated on the functional level with the acylation occurring either on the 2' OH (class I) or 3' OH (class II) of the ribose of the last nucleotide of tRNA.     

Molecular mechanism of the inhibitory effect of methylation outside the recognition sequence of restriction endonuclease Pvu II on its cleavage activity

In 1991, we found that methylation outside the Pvu II recognition sequence could partially inhibit its cleavage activity. To clarify the molecular mechanism, three plasmids with different methylation states were constructed. Then, together with the original one, four plasmids were digested with different amounts of Pvu II. Results show that methylation on both sites results in 90 % inhibition; moving the methylated site one base further away decreases the inhibitory effect to about 30 %; with the adjacent dam methylation site eliminated, the inhibitory effect disappears. The data suggest that the inhibition of cleavage activity caused by outside methylation is not “all or none”, and the degree of inhibition is dependent on the position and the number of methylated bases.     

Selective coupling with K+ currents of muscarinic acetylcholine receptor subtypes in NG108-15 cells

The primary structures of two muscarinic acetylcholine receptor (mAChR) species, designated as mAChR I and mAChR II, have been elucidated by cloning and sequence analysis of DNAs complementary to the porcine cerebral and cardiac messenger RNAs, respectively. mAChR I and mAChR II expressed in Xenopus oocytes differ from each other both in acetylcholine-induced response and in antagonist binding properties. These results, together with the differential tissue location of the two mAChR mRNAs, have indicated that pharmacologically distinguishable subtypes of the mAChR represent distinct gene products. The primary structures of two additional mammalian mAChR species, designated as mAChR III and mAChR IV, have subsequently been deduced from the nucleotide sequences of the cloned cDNAs or genomic DNAs. We report here that mAChR I and mAChR III expressed in NG108-15 neuroblastoma-glioma hybrid cells, but not mAChR II and mAChR IV, efficiently mediate phosphoinositide hydrolysis, activation of a Ca2+-dependent K+ current and inhibition of the M-current, a voltage-dependent K+ current sensitive to muscarinic agonists.     

Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code

The sequence of a 4,869 base-pair fragment of Drosophila melanogaster mitochondrial DNA is presented. It contains genes for cytochrome oxidase subunits I, II and III, ATPase subunit 6 and six tRNAs together with two unassigned reading frames. The gene organization differs from that of mammalian mitochondrial DNAs. Evidence is provided for a genetic code in which AGA codes for serine and the quadruplet ATAA is used in initiation of translation.