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Y Xu

Publications and source records attributed to Y Xu.

At least 955 records · Page 53Linked to original sources
PubMed1995

Evidence for distinct ligand-bound conformational states of the multifunctional Escherichia coli repressor of biotin biosynthesis.

The Escherichia coli repressor of biotin biosynthesis (BirA) is a unique transcriptional repressor which catalyzes synthesis of its own corepressor and catalyzes attachment of a cofactor to an essential metabolic enzyme. BirA both catalyzes synthesis of biotinyl-5'-AMP from the substrates ATP and biotin and transfer of the biotin moiety from the adenylate to a lysine residue of a subunit of the acetyl-CoA carboxylase. BirA-bio-5'-AMP, moreover, binds sequence specifically to the biotin operator to repress transcription of the biotin biosynthetic genes. Using a combination of kinetic measurements of binding of the two ligands, biotin and bio-5'-AMP, to BirA as well as proteolytic digestion experiments, we have found evidence for at least three discrete conformational states of BirA. Results of stopped-flow fluorescence measurements of association of both ligands with BirA indicate that the process involves initial formation of a collision complex followed by a slow conformational change. The kinetics of the conformational change are distinct for the two ligands and are the basis for the difference in the thermodynamic stabilities of the two protein-ligand complexes. Different rates of proteolytic digestion of apoBirA and complexes of BirA with the two ligands were also observed. Results of the combined approaches indicate that apoBirA, and the BirA-bio-5'-AMP and BirA-biotin complexes are conformationally distinct.

Adenosine Monophosphate↗
PubMed1995

X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.

BACKGROUND: Nucleoside diphosphate (NDP) kinases provide precursors for DNA and RNA synthesis. In mammals, these enzymes are also involved in cell regulations. Human NDP kinase B, product of the human nm23-H2 gene, is both an enzyme and a transcription factor. It activates transcription of the c-myc oncogene independently of its catalytic function, by binding to its promoter DNA. How do the two functions coexist? RESULTS: Recombinant human NDP kinase B was co-crystallized with GDP. The X-ray structure was solved at 2.0 A resolution by molecular replacement from the homologous Drosophila Awd protein. Both enzymes are homo-hexamers with a characteristic beta alpha beta beta alpha beta fold. GDP binds near the active site His118. The guanine base is in a surface cleft and interacts with the C terminus of another subunit. CONCLUSIONS: The beta alpha beta beta alpha beta fold, also present in the 'palm' domain of Escherichia coli DNA polymerase I and HIV reverse transcriptase, is both a mononucleotide- and a polynucleotide-binding fold. If NDP kinase B binds DNA in the same way as the polymerases, the enzyme must undergo a conformation change in order to carry out gene activation.

Amino Acid Sequence↗
PubMed1995

Desensitization and internalization of the m2 muscarinic acetylcholine receptor are directed by independent mechanisms.

The phenomenon of acute desensitization of G-protein-coupled receptors has been associated with several events, including receptor phosphorylation, loss of high affinity agonist binding, receptor:G-protein uncoupling, and receptor internalization. However, the biochemical events underlying these processes are not fully understood, and their contributions to the loss of signaling remain correlative. In addition, the nature of the kinases and the receptor domains which are involved in modulation of activity have only begun to be investigated. In order to directly measure the role of G-protein-coupled receptor kinases (GRKs) in the desensitization of the m2 muscarinic acetylcholine receptor (m2 mAChR), a dominant-negative allele of GRK2 was used to inhibit receptor phosphorylation by endogenous GRK activity in a human embryonic kidney cell line. The dominant-negative GRK2K220R reduced agonist-dependent phosphorylation of the m2 mAChR by approximately 50% and prevented acute desensitization of the receptor as measured by the ability of the m2 mAChR to attenuate adenylyl cyclase activity. In contrast, the agonist-induced internalization of the m2 mAChR was unaffected by the GRK2K220R construct. Further evidence linking receptor phosphorylation to acute receptor desensitization was obtained when two deletions of the third intracellular loop were made which created m2 mAChRs that did not become phosphorylated in an agonist-dependent manner and did not desensitize. However, the mutant mAChRs retained the ability to internalize. These data provide the first direct evidence that GRK-mediated receptor phosphorylation is necessary for m2 mAChR desensitization; the likely sites of in vivo phosphorylation are in the central portion of the third intracellular loop (amino acids 282-323). These results also indicate that internalization of the m2 receptor is not a key event in desensitization and is mediated by mechanisms distinct from GRK phosphorylation of the receptor.

Alleles↗
PubMed1995

Selective inhibition of thrombin receptor-mediated Ca2+ entry by protein kinase C beta.

Thrombin initiates many physiological processes in platelets and other megakaryocyte-lineage cells by interacting with surface receptors and generating rises in cytoplasmic Ca2+; these rises result from both Ca2+ release from intracellular stores and receptor-mediated Ca2+ entry. Regulators that limit Ca2+ entry after its initiation by thrombin have not been identified. In this study, prevention of expression of a single protein kinase C isoenzyme (PKC beta) by antisense cDNA overexpressed in HEL cells, a human megakaryoblastic cell line that expresses thrombin receptors, promotes thrombin receptor-mediated Ca2+ entry without altering thrombin-induced intracellular release of Ca2+. The cytoplasmic Ca2+ rise initiated by endoperoxide analogs was not affected by inhibiting PKC beta. Overexpression of a cDNA encoding wild-type PKC beta mutated to prevent recognition by the antisense cDNA abolished the enhancement of Ca2+ influx following thrombin. Thus, PKC beta appears to be a specific negative regulator of thrombin receptor-mediated Ca2+ entry.

Base Sequence↗
PubMed1995

Capillary electrophoretic enzyme immunoassay for digoxin in human serum.

The combined use of capillary electrophoretic (CE) separation and homogeneous enzyme immunoassay for analyzing drugs in hemolyzed, lipemic, or icteric serum samples was investigated. An FDA-approved EMIT assay kit for digoxin in human serum was used. After the enzyme immunoassay, the enzymatic reaction product (NADH) and remaining substrate (NAD+), together with internal standard (p-nitrophenol, NP), were electrokinetically injected into a polyacrylamide-coated electrophoresis capillary and separated under applied potential. Detection was made by monitoring the UV adsorption at wavelength of 260 nm. The digoxin level in human serum was determined by comparing the peak area ratio of NADH and NP to the ratios established by the known digoxin standards. In this study, the factors that influence the CE separation were also investigated. Under the optimum conditions, NADH, NAD+, and NP were separated at electric field strength of 438 V/cm in the coated capillary (100 microns x 57 cm) with 200 mM Tris-borate buffer (pH 7.9) containing 0.2% hydroxypropyl methylcellulose. CE analyses of serum samples spiked with NADH standards at concentrations of 100 and 400 microM resulted in detection variabilities of less than 2% and analytical recoveries of 98-102%. Both an internal calibration plot for NADH and a dose-response curve for digoxin in serum were constructed. Calibrator serum, patients' sera with hemolyzed, lipemic, and icteric interference factors, and other pigmented blood components (e.g., serum albumin, bilirubin, hemoglobin, uric acid, coproporphyrin, melanin, protoporphyrin IX, and uroprophyrin) demonstrated no interference in this method. The authors believed that this method is useful for analyzing digoxin in hemolyzed, lipemic, and icteric blood samples that are known to create problems in conventional EMIT assays and may be applicable to other EMIT-based assays for monitoring drugs in complex biological matrices.

Digoxin↗
PubMed1995

Lysophospholipids activate ovarian and breast cancer cells.

We have investigated the effects of phospholipids on activation and proliferation of ovarian and breast cancer cells. Lysophosphatidic acid (LPA), lysophosphatidylserine (LPS) and sphingosylphosphorylcholine (SPC) all induce transient increases in cytosolic free Ca2+ ([Ca2+]i) in both ovarian and breast cancer cell lines. The ability of LPA, LPS and SPC to induce increases in [Ca2+]i in ovarian and breast cancer cells is likely to be due to an interaction with cell-surface receptors as the increases in [Ca2+]i were: (1) due to release of calcium from intracellular stores and not from transmembrane uptake due to changes in permeability; (2) blocked by lanthanum and suramin which do not enter cells; (3) blocked by phorbol esters which interrupt increases in [Ca2+]i induced through a number of different receptors; and (4) not detected in freshly isolated peripheral blood mononuclear cells, indicating cell type specificity. In addition, increases in [Ca2+]i induced by LPA, LPS and SPC in ovarian and breast cancer cells completely self-desensitized and cross-desensitized each other, but did not block increases in [Ca2+]i induced by thrombin. Lysophosphatidylglycerol (LPG), but not other lysophospholipids, inhibited LPA- but not LPS- or SPC-induced increases in [Ca2+]i, suggesting that LPA may interact with a different receptor(s) to LPS or SPC and that their downstream signalling pathways converge or interact. LPA, SPC and LPS also induced rapid increases in tyrosine phosphorylation of specific cellular proteins, including p125FAK. Strikingly, LPA, but not LPS or SPC, induced activation of mitogen-activated protein (MAP) kinases. Despite an ability to activate similar intracellular signaling events, LPA, LPS and SPC exhibited markedly different effects on cell proliferation. Whereas LPA induced a significant increase in cell proliferation, LPS did not substantially alter cell proliferation and SPC inhibited cell proliferation. Surprisingly, phosphatidic acid (PA), which did not induce increases in [Ca2+]i, p125FAK activation or activation of MAP kinases, did induce proliferation of ovarian cancer cells, albeit at higher concentrations that LPA. The discordance between sensitivity to LPG, early biochemical events stimulated, and the eventual proliferation response combine to suggest that LPA probably utilizes a different receptor from LPS, SPC and PA. Therefore ovarian and breast cancer cells are sensitive to the effects of a number of different phospholipids which may play a role in the growth of these tumour cells in the cancer patient and are thus potential targets for therapy.

Breast Neoplasms↗
PubMed1995

Genetic and redox determinants of nitric oxide cytotoxicity in a Salmonella typhimurium model.

Paradoxically, nitric oxide (NO) has been found to exhibit cytotoxic, antiproliferative, or cytoprotective activity under different conditions. We have utilized Salmonella mutants deficient in antioxidant defenses or peptide transport to gain insights into NO actions. Comparison of three NO donor compounds reveals distinct and independent cellular responses associated with specific redox forms of NO. The peroxynitrite (OONO-) generator 3-morpholinosydnonimine hydrochloride mediates oxygen-dependent Salmonella killing, whereas S-nitrosoglutathione (GSNO) causes oxygen-independent cytostasis, and the NO. donor diethylenetriamine-nitric oxide adduct has no antibacterial activity. GSNO has the greatest activity for stationary cells, a characteristic relevant to latent or intracellular pathogens. Moreover, the cytostatic activity of GSNO may best correlate with antiproliferative or antimicrobial effects of NO, which are unassociated with overt cell injury. dpp mutants defective in active dipeptide transport are resistant to GSNO, implicating heterolytic NO+ transfer rather than homolytic NO. release in the mechanism of cytostasis. This transport system may provide a specific pathway for GSNO-mediated signaling in biological systems. The redox state and associated carrier molecules are critical determinants of NO activity.

Base Sequence↗
PubMed1995

Irreversible inhibitors of nicotinic acetylcholine receptors: isolation and structural characterization of the biologically active solvolysis products of bipinnatin-A and bipinnatin-C.

The lophotoxins irreversibly inhibit nicotinic acetylcholine receptors by covalent modification of Tyr190 in the alpha-subunits of the receptor. Previous studies have shown that the naturally occurring lophotoxin analogs bipinnatin-A, -B, and -C are actually inactive protoxins and that their ability to irreversibly inhibit nicotinic receptors is enhanced by preincubation in buffer. However, the ability of lophotoxin to irreversibly inhibit nicotinic receptors does not appear to be enhanced by preincubation in buffer. These observations led to the current effort to isolate and determine the structures of biologically active bipinnatins. Disappearance of the lophotoxins from solution followed a simple first-order exponential decay function. Lophotoxin, however, was approximately 40-fold more stable then bipinnatin-A, -B, or -C. Solvolysis of the bipinnatins, but not of lophotoxin, resulted in production of an equimolar amount of acetic acid at a rate similar to the rate of solvolysis, suggesting that the initial event in solvolysis of these toxins involves hydrolysis of an acetate ester. Proton NMR and fast-atom bombardment mass spectroscopy were used to confirm the structures of the active solvolysis products of bipinnatin-A and -C. Their structures and the relative pH insensitivity of the solvolysis reaction suggest that biological activation of the bipinnatins may proceed through an SN1 type of substitution reaction involving elimination of acetate followed by reaction of a carbocation intermediate with solvent.

Cell Line↗
PubMed1995

Phytochromes: photosensory perception and signal transduction.

The phytochrome family of photoreceptors monitors the light environment and dictates patterns of gene expression that enable the plant to optimize growth and development in accordance with prevailing conditions. The enduring challenge is to define the biochemical mechanism of phytochrome action and to dissect the signaling circuitry by which the photoreceptor molecules relay sensory information to the genes they regulate. Evidence indicates that individual phytochromes have specialized photosensory functions. The amino-terminal domain of the molecule determines this photosensory specificity, whereas a short segment in the carboxyl-terminal domain is critical for signal transfer to downstream components. Heterotrimeric GTP-binding proteins, calcium-calmodulin, cyclic guanosine 5'-phosphate, and the COP-DET-FUS class of master regulators are implicated as signaling intermediates in phototransduction.

Photoreceptor Cells↗
PubMed1995

Effects of tetrandrine on left ventricle hypertrophy in deoxycorticosterone acetate-salt hypertensive rats.

The effect of regression of left ventricular hypertrophy was studied in deoxycorticosterone-acetate-salt hypertensive rats (DOCA-salt hypertensive rats) treated with tetrandrine. Treatment with tetrandrine (by gastric intubation, 50 mg/kg per day for 9 weeks) lowered systolic blood pressure, left ventricular weight, Ca2+ of mitochondria, and markedly decreased the density (Bmax) and total number of dihydropyridine binding sites in hypertrophic left ventricle (P < 0.001). There was no difference between groups in dissociation constant (Kd) values of dihydropyridine binding sites. These facts indicate that tetrandrine decreased cardiac mass in DOCA-salt hypertensive rats through mechanisms that may be associated with the density and the total number of dihydropyridine binding sites, Ca2+ and blood pressure control.

Alkaloids↗
PubMed1995

Determination of plasma non-esterified fatty acids and triglyceride fatty acids by gas chromatography of their methyl esters after isolation by column chromatography on silica gel.

Non-esterified fatty acids (NEFA) and triglycerides were isolated from human plasma by column chromatography on silica gel. Eight principal fatty acids of each of these lipid classes were determined by gas chromatography of their methyl ester derivatives and quantified relative to multipoint standard curves. Within-day relative standard deviations for plasma non-esterified fatty acid and triglyceride fatty acid determinations were 2.4 and 3.2%, respectively. Day-to-day relative standard deviations for plasma non-esterified fatty acid and triglyceride fatty acid determinations were 1.4 and 1.1%, respectively. The total plasma concentration and the relative proportions of the eight non-esterified fatty acids determined by this method were significantly different from results obtained according to two generally accepted methods for direct plasma non-esterified fatty acid determination without a specific isolation step. These comparisons suggested that considerable fatty acid ester lipid hydrolysis occurred during these direct determination procedures, and that this hydrolysis resulted in 3-fold overestimation of plasma NEFA content by those methods. Measured levels of arachidonic acid are substantially overestimated by these direct determination methods in which non-esterified fatty acids are not isolated before derivatization.

Chromatography, Gas↗
PubMed1995

Sexual isolation in Drosophila melanogaster: a possible case of incipient speciation.

It is generally believed that Drosophila melanogaster has no closely related species with which it can produce the viable and fertile hybrids that are essential for the genetic analysis of speciation. Following the recent report of molecular differentiation between a Zimbabwe, Africa, population and two United States populations, we provide evidence that strong sexual isolation exists between the D. melanogaster population in Zimbabwe and populations of other continents. In the presence of males of their own kind, females from most isofemale lines of Zimbabwe would not mate with males from elsewhere; the reciprocal mating is also significantly reduced, but to a lesser degree. The genes for sexual behaviors are apparently polymorphic in Zimbabwe and postmating reproductive isolation between this and other populations has not yet evolved. Whole chromosome substitutions indicate significant genetic contributions to male mating success by both major autosomes, whereas the X chromosome effect is too weak to measure. In addition, the relative mating success between hybrid and pure line males supports the interpretation of strong female choice. These observations suggest that we are seeing the early stages of speciation in this group and that it is driven by sexual selection. The genetic and molecular tractability of D. melanogaster offers great promise for the detailed analysis of this apparent case of incipient speciation.

Animals↗
PubMed1995

ARE- and TRE-mediated regulation of gene expression. Response to xenobiotics and antioxidants.

Antioxidant response elements (AREs) containing 12-O-tetradecanoylphorbol-13-acetate response element (TRE) (perfect AP1) and TRE-like (imperfect AP1) elements mediate high basal transcription of the NAD(P)H:quinone oxidoreductase1 (NQO1) and glutathione S-transferase Ya genes in tumor cells and its induction in response to xenobiotics and antioxidants. Mutations in the human NQO1 gene ARE (hARE) revealed the requirement for two TRE or TRE-like elements arranged in inverse orientation at the interval of three base pairs and a GC box for optimal expression and beta-naphthoflavone induction of the NQO1 gene. A single TRE element from the human collagenase gene failed to respond to beta-naphthoflavone. These results demonstrate that ARE (2 x TRE or TRE-like elements)-containing detoxifying enzyme genes and not genes that contain 1 x TRE are responsive to xenobiotics and antioxidants. Bandshift assays showed shifting of a complex of more or less similar mobility with hARE and TRE that could be competed by each other. Mutations in the 3'-TRE of the NQO1 gene hARE eliminated binding of nuclear proteins to the hARE and resulted in the loss of basal and induced expression, indicating that 3'-TRE is the most important element within the hARE. 5'-TRE-like element within the NQO1 gene hARE is required for xenobiotic response but may not bind to the nuclear proteins by itself. The GC box located immediately following the 3'-TRE is required for optimal expression and induction of the NQO1 gene. The comparison of AREs from several different genes indicated the requirement for specific arrangement and spacing of two TRE and TRE-like elements within the AREs.

Antioxidants↗
PubMed1995

Substance P and bradykinin are natural inhibitors of CD13/aminopeptidase N.

Aminopeptidase N (EC 3.4.11.2) is an important enzyme that is involved in the degradation of regulatory peptides including enkephalins. We report here that purified and native membrane-bound aminopeptidase N will sequentially and completely hydrolyze both Leu-enkephalin and Met-enkephalin from the amino terminus. Both purified pig aminopeptidase N and the enzyme on live HL60 cells displayed similar Km values for enkephalin. The naturally occurring neuropeptides substance P and bradykinin, and the morphine agonist, morphiceptin, were not hydrolyzed by aminopeptidase N and each inhibited the enzymatic activity. Each of these peptides contains a proline at the second residue. The Ki values for substance P (0.44 microM), bradykinin (9.4 microM), and morphiceptin (169 microM) were obtained with the enzyme on live HL60 cells. The values for the purified enzyme from pig were similar. The potent inhibition of aminopeptidase N by substance P and bradykinin suggests that these peptides may be natural inhibitors of the enzyme.

Amino Acid Sequence↗
PubMed1995

Cyclic ADP-ribose-induced calcium release in sea urchin egg homogenates is a cooperative process.

Cyclic ADP-ribose (cADPR), an enzymatic product formed from NAD+ in sea urchin eggs and in several mammalian cell types, has been proposed as a second messenger for the regulation of cytosolic free Ca2+ concentration. Although cADPR induces Ca2+ release from an intracellular Ca2+ pool by a mechanism that differs from that used by inositol 1,4,5-trisphosphate, the precise action is unknown. We have analyzed the kinetics of cADPR-induced Ca2+ release at 15 degrees C in sea urchin egg homogenates using the calcium indicator fluo-3. In this system, Ca2+ release induced by cADPR was a positively cooperative process with a Hill coefficient of 1.8 +/- 0.32 (mean +/- SE, n = 15). We also examined the effect of caffeine, which potentiates the action of cADPR, on the kinetics of cADPR-induced Ca2+ release. Caffeine (3 mM) did not affect the degree of cooperativity induced by cADPR, but it did cause an increase in the apparent affinity of cADPR for its cellular target; the apparent Kd, derived from the kinetic analysis, decreased from 176 +/- 50 to 68 +/- 13 nM. We conclude that cADPR-induced Ca2+ release in sea urchin eggs is a cooperative process. A straightforward interpretation of the analysis is that opening of the Ca(2+)-release channel requires the binding of two molecules of cADPR (Hill coefficient of about 2). However, it is not yet known whether cADPR binds directly to the release channel. It is possible that potentiation of the action of cADPR by newly released Ca2+ could also contribute to the observed cooperative effect.

Adenosine Diphosphate Ribose↗
PubMed1995

Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with [1-14C]bromopyruvate and site-directed mutagenesis.

Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of adenosine 5'-triphosphate (ATP), orthophosphate (Pi), and pyruvate with adenosine 5'-monophosphate (AMP), pyrophosphate (PPi), and phosphoenolpyruvate (PEP). The reaction takes place according to the following steps: (1) E+ATP+P(i)<-->E-PP.AMP.P(i), (2) E-PP.AMP.P(i)<-->E-P+AMP+PP(i), and (3) E-P+pyruvate<-->E+PEP, where E represents free enzyme; E-PP, pyrophosphorylenzyme; and E-P, phosphorylenzyme. Steps 1 and 2 comprise the nucleotide partial reaction, and step 3 comprises the pyruvate partial reaction. The present studies were carried out to locate amino acid residues within the primary structure of Clostridium symbiosum PPDK participating in the catalysis of the pyruvate partial reaction. The enzyme was treated with the affinity label [1-14C]bromopyruvate, reduced with NaBH4, proteolyzed with trypsin, and chromatographed on an HPLC column. The radiolabeled tryptic peptide isolate was sequenced to reveal Cys 831 as the site of alkylation. Using PCR techniques Cys 831 was replaced by Ala, and the C831A PPDK mutant formed was then subjected to kinetic analysis. Rapid quench studies of single turnover reactions on the enzyme showed that the mutant is as efficient as wild-type PPDK in catalyzing the nucleotide partial reaction while it is unable to catalyze the pyruvate partial reaction. These results were interpreted as evidence for a role of Cys 831 in pyruvate/PEP binding and/or catalysis.

Affinity Labels↗