bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton stoichiometry of the overexpressed uracil symport of the yeast Saccharomyces cerevisiae
Authors: EDDY A. Alan , HOPKINS Pamela 
Published: August 2015

Information about the molecular biology of the uracil carrier of Saccharomyces cerevisiae is now available but its properties as a symport are unexplored. We have now studied its proton stoichiometry at pH 6.5, 4.8 and 4.2, in a yeast strain overexpressing the symport and unable to metabolize uracil. After the depletion of cellular ATP, uracil uptake followed an approximately exponential time course to reach a plateau. Proton uptake was then indistinguishable from the basal rate shown in controls without added uracil. It was concluded that more than 87% of the uracil flux through the system was coupled to symported protons. Because the basal rate was a significant fraction of the total rate of proton uptake at pH 4.2 or 4.8, the ratio of the proton and uracil flows could not be defined uniquely during the initial near-linear phase of uptake. However, the average rate of proton uptake during increasing time intervals up to 120 s was shown to be a linear function of the corresponding average rate of uracil uptake. This relationship, defining approx. 90% of the eventual uracil uptake, was used to deduce the mean proton stoichiometry as approx. 3 at pH 4.2, falling to near 2 at pH 6.5. The rate of uracil uptake increased 4-fold when the negative proton gradient (ΔµH) acting across the plasma membrane increased from 60 to 200 mV. The rate fell markedly after depolarization by KCl. The maximum uracil gradient (ΔµS) was less affected by depolarization. The ratio ΔµS/ΔµH fell from approx. 2 to near 1 as ΔµH increased in the above range. In contrast with the starved yeast, uracil accumulation during energy metabolism followed a pump-leak model.
Identification of Glu-120 as the catalytic nucleophile in Streptomyces lividans endoglucanase CelB
Authors: ZECHEL David L. , HE Shouming , DUPONT Claude , WITHERS Stephen G. 
Published: August 2015

Streptomyces lividans CelB is a family-12 endoglucanase that hydrolyses cellulose with retention of anomeric configuration. A recent X-ray structure of the catalytic domain at 1.75 Å resolution has led to the preliminary assignment of Glu-120 and Glu-203 as the catalytic nucleophile and general acid–base respectively [Sulzenbacher, Shareck, Morosoli, Dupont and Davies (1997) Biochemistry 36, 16032–16039]. The present study confirms the identity of the nucleophile by trapping the glycosyl-enzyme intermediate with the mechanism-based inactivator 2´,4´-dinitrophenyl 2-deoxy-2-fluoro-β-d-cellobioside (2FDNPC). The kinetics of inactivation proceeded in a saturable fashion, yielding the parameters kinact = 0.29±0.02 min-1 and Kinact = 0.72±0.08 mM. Uncompetitive inhibition was observed at high concentrations of 2FDNPC (Ki = 9±1 mM), a behaviour that was also observed with the substrate 2´,4´-dinitrophenyl β-d-cellobioside (kcat = 40±1 s-1, Km = 0.35±0.03 mM, Ki = 24±4 mM). Protection against inactivation was afforded by the competitive inhibitor cellobiose. The electrospray ionization (ESI) mass spectrum of the intact labelled CelB indicated that the inactivator had labelled the enzyme stoichiometrically. Reactivation of the trapped intermediate occurred spontaneously (kH2O = 0.0022 min-1) or via transglycosylation, with cellobiose acting as an acceptor ligand (kreact = 0.024 min-1, Kreact = 54 mM). Digestion of the labelled enzyme by pepsin followed by LC–ESI–tandem MS (MS–MS) operating in neutral loss mode identified a labelled, singly charged peptide of m/z 947.5 Da. Isolation of this peptide by HPLC and subsequent collision-induced fragmentation by ESI–MS–MS produced a daughter-ion spectrum that corresponded to a sequence (QTEIM) containing Glu-120. The nucleophile Glu-120 and the putative acid–base catalyst Glu-203 are conserved in all known family-12 sequences.
Recombinant human glutathione S-transferases catalyse enzymic isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro
Authors: CHEN Hao , JUCHAU Mont R. 
Published: August 2015

The steric conversion of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) has been proposed as an activation mechanism for the observed therapeutic and teratogenic activities of 13-cRA. Here we have investigated the catalysis of isomerization of 13-cRA to t-RA by recombinant human glutathione S-transferases (GSTs). Substrate was incubated with GST in 0.1 M sodium phosphate buffer, pH 7.5, at 37 °C in total darkness. The t-RA generated was measured quantitatively by HPLC. Under the reaction conditions used, GSTP1–1 was far more effective than human GSTM1–1 or human GSTA1–1 in catalysing the isomerization reaction. The reaction catalysed by GSTP1–1 showed substrate saturation and the Km and Vmax values for the reaction were approx. 7 µM and 650 pmol/min per nmol respectively. The reaction rate increased linearly with increasing enzyme concentration. The reaction was inhibited both by heat treatment and by S-decylglutathione (a potent inhibitor of transferase activity associated with GST). Additions of polyclonal rabbit antiserum for human GSTP1–1 to the reaction resulted in a significant decrease in generation of t-RA (70–80%). In addition, ethacrynic acid, a selective substrate for Pi isoforms of GST, also inhibited the isomerization of 13-cRA to t-RA catalysed by GSTP1–1. Under the same reaction conditions, GSTP1–1 was much less effective in catalysing the steric conversion of 9-cis-retinoic acid to t-RA, indicating that the enzyme was stereospecific for the conversion of 13-cRA to t-RA. These observations suggest that enzymic catalysis was the primary mechanism for the GSTP1–1-dependent conversion of 13-cRA to t-RA. Reactions catalysed by a purified rat hepatic GST Pi isoenzyme proceeded more slowly than reactions catalysed by human GSTP1–1. Comparative studies also showed that there were marked species differences in catalytic activities between various purified mammalian hepatic GST mixtures.
Direct demonstration of a specific interaction between cyclophilin-D and the adenine nucleotide translocase confirms their role in the mitochondrial permeability transition
Authors: WOODFIELD Kuei , RÜCK Alexander , BRDICZKA Dieter , HALESTRAP Andrew P. 
Published: August 2015

A fusion protein between cyclophilin-D (CyP-D) and glutathione S-transferase (GST) was shown to bind to purified liver inner mitochondrial membranes (IMMs) in a cyclosporin A (CsA)-sensitive manner. Binding was enhanced by diamide treatment of the IMMs. Immobilized GST–CyP-D avidly bound a single 30 kDa protein present in Triton X-100-solubilized IMMs; immunoblotting showed this to be the adenine nucleotide translocase (ANT). Binding was prevented by pretreatment of the CyP-D with CsA, but not with cyclosporin H. Purified ANT also bound specifically to GST–CyP-D, but porin did not, even in the presence of ANT.
Purification of human dihydro-orotate dehydrogenase and its inhibition by A77 1726, the active metabolite of leflunomide
Authors: BRUNEAU Jean-Michel , YEA Christopher M. , SPINELLA-JAEGLE Sylviane , FUDALI Claude , WOODWARD Katherine , ROBSON Peter A. , SAUTÈS Catherine , WESTWOOD Robert , KUO Elizabeth A. , WILLIAMSON Richard A. , RUUTH Erik 
Published: August 2015

Leflunomide is currently in phase-III clinical trials for the treatment of rheumatoid arthritis. In this study, we have focused our efforts on the study of the mechanism of action of the active metabolite of leflunomide, A77 1726, in cells and tissue of human origin. The human high-affinity binding protein for radiolabelled A77 1726 was purified from solubilized U937 membranes by following the binding activity through the purification process and was characterized as the mitochondrial enzyme dihydro-orotate dehydrogenase (DHO-DH). The human and murine enzyme displayed identical pI and molecular mass values on SDS/PAGE (43 kDa), which contrasts notably with previous reports suggesting a molecular mass of 50 kDa for the human enzyme. DHO-DH activity was inhibited by A77 1726 and its analogue HR325 with similar potency in U937 and human spleen membrane preparations. HR325 was found to be anti-proliferative for phytohaemagglutinin-stimulated human peripheral blood mononuclear cells, at the same concentrations that caused accumulation of DHO and depletion of uridine. Supplementation of the cultures with exogenous uridine led to partial abrogation of the anti-proliferative effect. This is in line with our recent demonstration that the anti-proliferative effect in vitro of A77 1726 on lipopolysaccharide-stimulated mouse spleen cells was mediated by DHO-DH inhibition [Williamson, Yea, Robson, Curnock, Gadher, Hambleton, Woodward, Bruneau, Hambleton, Moss et al., (1995) J. Biol. Chem. 270, 22467–22472]. Thus, DHO-DH inhibition by A77 1726 and its analogues is responsible for the anti-proliferative effects in vitro of the compounds on human cells and is likely to be responsible for some of its effects in vivo.
Mouse annexin V genomic organization includes an endogenous retrovirus
Authors: RODRIGUEZ-GARCIA Maria-Isabel , MORGAN Reginald O. , FERNANDEZ Maria-Rosa , BANCES Patricia , FERNANDEZ Maria-Pilar 
Published: August 2015

Mouse annexin V genomic clones were characterized by restriction analysis, Southern blotting and DNA sequencing. The entire gene spans close to 50 kb of the mouse genome and contains 14 exons ranging in size from 31 bp for exon 2 to 482 bp for exon 13 up to the polyadenylation site. Intron sizes range from 111 bp for intron 1b to more than 17 kb for intron 2. Non-coding exon 1 is present in two alternative forms separated by approx. 7.4 kb, and the two promoters associated with exons 1a and 1b are quite distinct. The upstream promoter has a TATA box and may direct the limited, tissue-specific expression of mRNA transcripts containing exon 1a. The downstream, TATA-less promoter has high G+C content, and exon 1b predominates among abundantly expressed mRNA species. The conservation of certain cis-elements, including Sp1, AP2, γ-IRE and NF-IL6, in orthologous species of annexin V genes points to their possible role in trans-acting protein factor binding and gene regulation. Primer-extension analysis revealed multiple origins for transcription, with principal start sites 100–150 bp upstream of the ATG start codon in exon 2. Intron 4 was longer than that previously identified in the orthologous rat gene due to the integration of an apparently complete copy of the murine endogenous retrovirus element, MuERV-L. Phylogenetic analysis of annexin V from 12 species and the presence of neighbouring loci with paralogous counterparts linked to annexin VI pointed to the common ancestry of these genes via chromosomal duplication more than 600 million years ago.
Structural aspects of the effectiveness of bisphosphonates as competitive inhibitors of the plant vacuolar proton-pumping pyrophosphatase
Authors: GORDON-WEEKS Ruth , PARMAR Saroj , DAVIES T. G. Emyr , LEIGH Roger A. 
Published: August 2015

The bisphosphonates (general structure PO3-R-PO3) competitively inhibit soluble and membrane-bound inorganic pyrophosphatases (PPases) with differing degrees of specificity. Aminomethylenebisphosphonate (AMBP; HC(PO3)2NH2) is a potent, specific inhibitor of the PPase of higher plant vacuoles (V-PPase). To explore the possibility of constructing photoactivatable probes from bisphosphonates to label the active site of V-PPase we analysed the effects of different analogues on the hydrolytic and proton pumping activity of the enzyme. Bisphosphonates with a range of structures inhibited competitively and the effects on PPi hydrolysis correlated with the effects on proton pumping. Low-molecular-mass bisphosphonates containing hydrophilic groups (α-NH2 or OH) were the most effective, suggesting that the catalytic site is in a restricted polar pocket. Bisphosphonates containing a benzene ring were less active but the introduction of a nitrogen atom into the ring increased activity. Compounds of the general formula NH2(CH2)nC(PO3)2OH were more inhibitory than compounds of the H(CH2)nC(PO3)2NH2, NH2(CH2)nC(PO3)2NH2 or OH(CH2)nC(PO3)2NH2 series, with activity decreasing as n increased. A nitrogen atom in the carbon chain increased activity but activity was decreased by the presence of an oxygen atom. An analogue with a ring attached via a four-carbon chain, which included an amide linkage and a hydroxy group on the α-carbon atom, inhibited competitively (Ki = 62.0 µM), suggesting that it may be possible to design bisphosphonate inhibitors which contain a photoactivatable azido group for photoaffinity labelling of V-PPase active site.
Novel peptide inhibitor of ecto-ADP-ribosyl cyclase of bone marrow stromal cell antigen-1 (BST-1/CD157)
Authors: SATO Atsushi , YAMAMOTO Sumie , ISHIHARA Katsuhiko , HIRANO Toshio , JINGAMI Hisato 
Published: August 2015

cADP-ribose, which is produced by ecto-ADP-ribosyl cyclase of CD38 or bone marrow stromal cell antigen-1 (BST-1), is a key regulator of Ca2+-induced calcium release in an Ins(1,4,5)P3-independent manner. In the present study, we have identified a specific peptide inhibitor for ADP-ribosyl cyclase of BST-1. A 15-mer random peptide phage library was screened with a soluble form of BST-1 expressed in baculovirus-infected insect cells. After biopanning, two potent sequences reactive towards BST-1 were isolated. The two synthetic peptides corresponding to the identified sequences were shown to antagonize each other's ability to inhibit the binding of the two isolated phage to BST-1, suggesting that they bind at a common binding site on BST-1. One of the peptides (SNP-1) was shown to inhibit ADP-ribosyl cyclase activity of BST-1 in an uncompetitive manner with a Ki value of 180±40 nM (n = 3). SNP-1 also inhibited cyclic ADP-ribose hydrolase activity of BST-1 dose-dependently. Selected phage did not cross-react with a soluble form of CD38. SNP-1 did not show any inhibitory effect on ADP-ribosyl cyclase activity of CD38, and therefore this peptide inhibitor will be useful to serve as a starting tool for understanding the roles of these intriguing ecto-enzymes. This is the first report of a specific ADP-ribosyl cyclase inhibitor.
Long-term maintenance of low concentrations of fructose for the study of hepatic glucose phosphorylation
Authors: PHILLIPS John W. , HENLY Debra C. , BERRY Michael N. 
Published: August 2015

The stimulation of glucose phosphorylation in isolated hepatocytes by low fructose concentrations is transient due to the rapid metabolism of fructose. To prolong this stimulatory effect fructose was enzymically generated in the incubation medium from either sucrose with invertase or inulin with inulinase. A maximal rate of glucose phosphorylation was achieved when fructose was formed at at least 0.01 µmol/min, which maintained a concentration of 70 µM fructose in the medium. In the presence of a fructose concentration of 70 µM, the rate of phosphorylation with 5 mM glucose was doubled and remained constant over a 2.5 h period. Under these conditions the rate of glycolysis was increased more than 3-fold. The stimulation of flux through glucokinase by low concentrations of fructose decreased the proportion of glucose phosphorylated, which was cycled between glucose and glucose 6-phosphate, and increased the proportion that was glycolysed. The method described for maintaining the stimulation of glucose phosphorylation by isolated hepatocytes over prolonged incubation periods is especially suited to the further study of the control of glucokinase activity, in particular how the variation of flux through glucokinase affects the flux through all the pathways that utilize the product, glucose 6-phosphate.
Substitution of Asp-309 by Asn in the Arg-Asp-Pro (RDP) motif of Acetobacter diazotrophicus levansucrase affects sucrose hydrolysis, but not enzyme specificity
Authors: BATISTA Frank R. , HERNÁNDEZ Lázaro , FERNÁNDEZ Julio R. , ARRIETA Juan , MENÉNDEZ Carmen , GÓMEZ Raúl , TÁMBARA Yanet , PONS Tirso 
Published: August 2015

β-Fructofuranosidases share a conserved aspartic acid-containing motif (Arg-Asp-Pro; RDP) which is absent from α-glucopyranosidases. The role of Asp-309 located in the RDP motif of levansucrase (EC 2.4.1.10) from Acetobacter diazotrophicus SRT4 was studied by site-directed mutagenesis. Substitution of Asp-309 by Asn did not affect enzyme secretion. The kcat of the mutant levansucrase was reduced 75-fold, but its Km was similar to that of the wild-type enzyme, indicating that Asp-309 plays a major role in catalysis. The two levansucrases showed optimal activity at pH 5.0 and yielded similar product profiles. Thus the mutation D309N affected the efficiency of sucrose hydrolysis, but not the enzyme specificity. Since the RDP motif is present in a conserved position in fructosyltransferases, invertases, levanases, inulinases and sucrose-6-phosphate hydrolases, it is likely to have a common functional role in β-fructofuranosidases.
Determination of the calcium-binding sites of the C2 domain of protein kinase Cα that are critical for its translocation to the plasma membrane
Authors: CORBALÁN-GARCÍA Senena , RODRÍGUEZ-ALFARO José A. , GÓMEZ-FERNÁNDEZ Juan C. 
Published: August 2015

The C2 domain is a conserved protein module present in various signal-transducing proteins. To investigate the function of the C2 domain of protein kinase Cα (PKCα), we have generated a recombinant glutathione S-transferase-fused C2 domain from rat PKCα, PKC-C2. We found that PKC-C2 binds with high affinity (half-maximal binding at 0.6 µM) to lipid vesicles containing the negatively charged phospholipid phosphatidylserine. When expressed into COS and HeLa cells, most of the PKC-C2 was found at the plasma membrane, whereas when the cells were depleted of Ca2+ by incubation with EGTA and ionophore, the C2 domain was localized preferentially in the cytosol. Ca2+ titration was performed in vivo and the critical Ca2+ concentration ranged from 0.1 to 0.32 µM. We also identified, by site-directed mutagenesis, three aspartic residues critical for that Ca2+ interaction, namely Asp-187, Asp-246 and Asp-248. Mutation of these residues to asparagine, to abolish their negative charge, resulted in a domain expressed as the same extension as wild-type protein that could interact in vitro with neither Ca2+ nor phosphatidylserine. Overexpression of these mutants into COS and HeLa cells also showed that they cannot localize at the plasma membrane, as demonstrated by immunofluorescence staining and subcellular fractionation. These results suggest that the Ca2+-binding site might be involved in promoting the interaction of the C2 domain of PKCα with the plasma membrane in vivo.
Isolation of a laminin-binding protein from the protozoan parasite Leishmania donovani that may mediate cell adhesion
Authors: GHOSH Abhijit , BANDYOPADHYAY Keya , KOLE Labanyamoy , DAS Pijush K. 
Published: August 2015

Extracellular matrix (ECM)-binding proteins on the surface of Leishmania are thought to play a crucial role in the onset of leishmaniasis, as these parasites invade mononuclear phagocytes in various organs after migrating through the ECM. In a previous report, we presented several lines of evidence suggesting that Leishmania has a specific receptor for laminin, a major ECM protein, with a Kd in the nanomolar range. Here we describe the identification, purification and biochemical characterization of the Leishmania laminin receptor. When the outer membrane proteins of L. donovani were blotted on to nitrocellulose paper and probed with laminin, a prominent laminin-binding protein of 67 kDa was identified. The purified protein was isolated by a three-step process involving DEAE–cellulose, Con A (concanavalin A)–Sepharose and laminin–Sepharose affinity chromatography and was used to raise a monospecific antibody. The same protein was obtained when parasite membrane extracts were adsorbed to antibody affinity matrix and eluted with glycine. The affinity-purified protein bound to laminin in a detergent-solubilized form as well as after integration into artificial bilayers, and was subsequently characterized as an integral membrane protein. Metaperiodate oxidation and metabolic inhibition of glycosylation studies indicate the binding protein to be glycoprotein in nature and that N-linked oligosaccharides play a part in the interaction of laminin with the binding protein. Surface-labelled parasites attached to microtitre wells coated with laminin and the 67 kDa protein blocked the adhesion to laminin substrate. We propose that the 67 kDa protein is an adhesin involved in the attachment of Leishmaniato host tissues.
Cloning and characterization of a simian UDP-glucuronosyltransferase enzyme UGT2B20, a novel C19 steroid-conjugating protein
Authors: BARBIER Olivier , BÉLANGER Alain , HUM Dean W. 
Published: August 2015

Steroid glucuronidation by UDP-glucuronosyltransferase (UGT) enzymes is a mechanism leading to catabolism and elimination of steroid hormones. To establish an animal model to investigate the conjugation of steroids by UGT enzymes, previous results revealed that simian and human are unique in having high levels of circulating androsterone glucuronide and androstane-3α,17β-diol (3d-Diol) glucuronide. A cDNA, UGT2B20, was isolated from cynomolgus monkey liver and prostate libraries. The cDNA was 2075 bp in length and contained an open reading frame of 1590 bp, encoding a protein of 530 amino acid residues. The UGT2B20 clone was transfected and stably expressed in the human embryo kidney HK293 cell line, and the transferase activity of UGT2B20 was tested with 73 compounds. This enzyme was shown to be active with androgens, such as testosterone, dihydrotestosterone (DHT) and 3α-Diol, and on catecholoestrogens including 1,3,5,10-oestratriene-3,4-diol-17-one. Kinetic analysis performed with intact cells yielded apparent Km values of 1.1, 2.3 and 4.6 µM for 3α-Diol, DHT and testosterone respectively. Reverse transcriptase-PCR analysis demonstrated that UGT2B20 transcript is expressed in several tissues including the liver, prostate, kidney, epididymis and adrenal of the cynomolgus monkey. Amino acid sequence alignment shows that the UGT2B20 protein is 92% identical with UGT2B15. Both enzymes have similar apparent Km values for DHT and 3α-Diol, and demonstrate similar transcript tissue distribution. The characterization of simian UGT2B20 as a structural and functional homologue of human UGT2B15 further demonstrates the similarities of steroid glucuronidation in these two species, and indicates the relevance of using the monkey as an animal model to study and understand steroid glucuronidation in extrahepatic-steroid target tissues.