bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactions of nitric oxide with mitochondrial cytochrome c: a novel mechanism for the formation of nitroxyl anion and peroxynitrite
Authors: SHARPE Martyn A. , COOPER Chris E. 
Published: August 2015

The aerobic reactions of nitric oxide with cytochrome c were analysed. Nitric oxide (NO) reacts with ferrocytochrome c at a rate of 200 M-1 s-1 to form ferricytochrome cand nitroxyl anion (NO-). Ferricytochrome c was detected by optical spectroscopy; NO- was detected by trapping with metmyoglobin (Mb3+) to form the EPR-detectable Mb–nitrosyl complex, and by the formation of dimers in yeast ferrocytochrome cvia cross-linking of the free cysteine residue. The NO- formed subsequently reacted with oxygen to form peroxynitrite, as measured by the oxidation of dihydrorhodamine 123. NO binds to ferricytochrome c to form the ferricytochrome c-NO complex. The on-rate for this reaction is 1.3±0.4×103 M-1·s-1, and the off-rate is 0.087±0.054 s-1. The dissociation constant (Kd)of the complex is 22±7 µM. These reactions of NO with cytochrome c are likely to be relevant to mitochondrial metabolism of NO. Ferricytochrome c can act as a reversible sink for excess NO in the mitochondria. The reduction of NO to NO- by ferrocytochrome cmay play a role in the irreversible inhibition of mitochondrial oxygen consumption by peroxynitrite. It is generally assumed that peroxynitrite would be formed in mitochondria via the reaction of NO with superoxide. The finding that NO- is formed from the reaction of NO and ferrocytochrome c provides a means of producing peroxynitrite in the absence of superoxide, via the reaction of NO- with oxygen.
Assembly of flammutoxin, a cytolytic protein from the edible mushroom Flammulina velutipes, into a pore-forming ring-shaped oligomer on the target cell
Authors: TOMITA Toshio , ISHIKAWA Dai , NOGUCHI Takayasu , KATAYAMA Eisaku , HASHIMOTO Yohichi 
Published: August 2015

Flammutoxin has been previously isolated as a cardiotoxic and cytolytic polypeptide of 22 or 32 kDa from the fruiting bodies of the edible mushroom Flammulina velutipes. In the present study, we purified flammutoxin as a single haemolytic protein of 31 kDa and studied the mode of its cytolytic action. (1) Flammutoxin caused efflux of potassium ions from human erythrocytes and swelling of the cells before haemolysis. (2) Flammutoxin did not lyse human erythrocytes in the presence of non-electrolytes with hydrodynamic diameters of &gt; 5.0 nm, although it caused leakage of potassium ions and swelling of the cells under the same conditions. (3) Experiments including solubilization of cell-bound toxin with 2% (w/v) SDS at 20 °C and subsequent Western immunoblots showed that flammutoxin formed a band corresponding to 180 kDa under the conditions where it lysed erythrocytes. (4) Electron microscopy of flammutoxin-treated human erythrocytes revealed the presence of a ring-shaped structure with outer and inner diameters of 10 and 5 nm, respectively, on the cells. (5) A ring-shaped toxin oligomer of the same dimensions was solubilized from the toxin-treated human erythrocytes with 2% (w/v) SDS at 20 °C and isolated by a sucrose-gradient ultracentrifugation. These data indicated that flammutoxin assembles into a ring-shaped oligomer possessing a hydrophilic pore of 4–5 nm on target cells.
Intestinal absorption of bile acids: paradoxical behaviour of the 14 kDa ileal lipid-binding protein in differential photoaffinity labelling
Authors: KRAMER Werner , CORSIERO Daniel , FRIEDRICH Michael , GIRBIG Frank , STENGELIN Siegfried , WEYLAND Claudia 
Published: August 2015

Photoaffinity labelling of brush border membrane vesicles from rabbit ileum with radiolabelled 3,3-azo and 7,7-azo derivatives of taurocholate identified integral membrane proteins of molecular masses 93 and 46 kDa, as well as a 14 kDa peripheral membrane protein, as components of the ileal Na+/bile acid transport system [Kramer, Girbig, Gutjahr, Kowalewski, Jouvenal, Müller, Tripier and Wess (1993) J. Biol. Chem. 268, 18035–18046]. Differential photoaffinity labelling in the presence of non-radiolabelled bile acid derivatives led, as expected, to a concentration-dependent decrease in the extent of labelling of the 93 and 46 kDa transmembrane proteins, which are the monomeric and dimeric forms of the ileal bile acid transporter protein. The extent of labelling of the 14 kDa ileal lipid-binding protein (ILBP), however, increased on the addition of unlabelled bile acids, the increase being dependent on the structure of the bile acid added. The possibility of artifacts was excluded by photoaffinity labelling experiments in the frozen state as well as by model calculations. The experimental results suggest that the binding of bile acids to ILBP can increase the affinity of ILBP for bile acids. These results would be in accordance with a substrate-load modification of transport activity and a positive-feedback regulation mechanism for active uptake of bile acid in the ileum.
4-Aminobutyrate (GABA) transporters from the amine-polyamine-choline superfamily: substrate specificity and ligand recognition profile of the 4-aminobutyrate permease from Bacillus subtilis
Authors: BRECHTEL Casey E. , KING Steven C. 
Published: August 2015

A previous study [Ferson, Wray and Fisher (1996) Mol. Microbiol. 22, 693–701] has shown that transposon-mediated disruption of a protein 47% identical to the Escherichia coli GABA (4-aminobutyrate) transporter abolishes the ability of nitrogen-limited culture conditions to induce expression of a GABA transport activity in Bacillus subtilis. Here it is demonstrated directly that the B. subtilis GABA permease (gabP) gene can complement the transport defect in the gabP-negative E. colistrain. Unexpectedly, the ligand-recognition profile of the B. subtilis GabP was found to differ substantially from that of the highly homologous E. coli GabP. Unlike the E. coli GabP, the B. subtilis GabP: (i) exhibits approx. equal preference for the 3-carbon (β-alanine, Km = 9.6 µM) and the 4-carbon (GABA, Km = 37 µM) amino acids, and (ii) resists inhibition by bulky, conformationally constrained compounds (e.g. nipecotic acid, guvacine), which are active against GABA transporters from brain. The present study shows additionally that the B. subtilis GabP can translocate several open-chain GABA analogues (3-aminobutyrate, 3-aminopropanoate, cis-4-aminobutenoate) across the membrane via counterflow against [3H]GABA. Thus, consistent with the idea that the ligand-recognition domain of the B. subtilis GabP is less spacious than that of the close homologue from E. coli, the former exhibits more stringent requirements than the latter for substrate recognition and translocation. These distinct functional characteristics of the E. coli and B. subtilis GABA transporters provide a basis by which to identify ligand-recognition domains within the amine-polyamine-choline transporter superfamily.
Linear and cyclic peptides as substrates and modulators of P-glycoprotein: peptide binding and effects on drug transport and accumulation
Authors: SHAROM Frances J. , LU Peihua , LIU Ronghua , YU Xiaohong 
Published: August 2015

One cause of multidrug resistance (MDR) in human cancers is the overexpression of the P-glycoprotein multidrug transporter, a member of the ABC superfamily of membrane proteins. Natural products and chemotherapeutic drugs are pumped out of the cell by P-glycoprotein in an ATP-dependent fashion. There is growing evidence that many hydrophobic peptides are also P-glycoprotein substrates. With the use of a fluorescence-quenching assay, we have shown that some linear and cyclic hydrophobic peptides interact with P-glycoprotein, whereas others do not. The measured values of the quenching constant, Kq, for interaction of peptides with P-glycoprotein ranged from 200 nM for cyclosporine A to 138 µM for the tripeptide N-acetyl-leucyl-leucyl-norleucinal. Peptides that interacted with P-glycoprotein in the fluorescence assay also blocked colchicine transport into plasma membrane vesicles from MDR cells. The values of Dm, the peptide concentration causing 50% inhibition of drug uptake, were highly correlated with the values of Kq, over three orders of magnitude. The P-glycoprotein ATPase stimulation/inhibition profile of the peptides was not helpful in making a quantitative assessment of the ability of a peptide to interact with P-glycoprotein or to block drug transport. Some hydrophobic peptides were able to restore accumulation in MDR cells of the chemotherapeutic drug daunorubicin and the fluorescent dye rhodamine 123 to the levels observed in the drug-sensitive parent. Peptides that interacted with P-glycoprotein also displayed a relatively low overall toxicity to intact MDR cells, and inhibited drug transport at concentrations below the toxic range. Hydrophobic peptides should be given serious consideration for development as clinical chemosensitizing agents.
Molecular cloning and characterization of Ca2+-dependent inducible nitric oxide synthase from guinea-pig lung
Authors: SHIRATO Manabu , SAKAMOTO Tohru , UCHIDA Yoshiyuki , NOMURA Akihiro , ISHII Yukio , IIJIMA Hiroaki , GOTO Yukio , HASEGAWA Shizuo 
Published: August 2015

We have isolated a full-length cDNA for an inducible nitric oxide synthase (iNOS) from guinea-pig lung. The cDNA has a 3447 bp open reading frame encoding 1149 amino acid residues. The deduced amino acid sequence is approx. 80% identical with iNOS of human epithelial cells and murine macrophages. Consensus recognition sites for cofactors are highly conserved. COS cell lysate transfected with the guinea-pig iNOS shows significant levels of nitric oxide synthase (NOS) activity, and this is inhibited by 79% by chelation of Ca2+ ions. The NOS activity is restored in a concentration-dependent manner by increasing the free Ca2+ level. The NOS activity is also inhibited by trifluoperazine, a calmodulin antagonist, which suggests that the Ca2+ dependence is due to Ca2+-dependent calmodulin binding to the enzyme. Northern blot analysis reveals that the cloned iNOS mRNA is expressed in the lung and the colon in normal guinea pigs. Stimulation in vivo by lipopolysaccharide induces the expression of iNOS in the kidney, the spleen and the colon, but in the lung the same stimulation decreases its expression. These results suggest that the cloned guinea-pig iNOS is distinct in characteristics and expression from previously described iNOS forms.
Transcriptional activation of the haem oxygenase-1 gene by cGMP via a cAMP response element/activator protein-1 element in primary cultures of rat hepatocytes
Authors: IMMENSCHUH Stephan , HINKE Vera , OHLMANN Andreas , GIFHORN-KATZ Susanne , KATZ Norbert , JUNGERMANN Kurt , KIETZMANN Thomas 
Published: August 2015

The expression of the rate-limiting enzyme of haem degradation, haem oxygenase-1 (HO-1), can be induced by various stimuli, including lipopolysaccharide, tumour necrosis factor α and NO. The NO signal can be transmitted by cGMP, therefore this study was aimed at testing the activation of the HO-1 gene by cGMP. In primary cultures of rat hepatocytes, both HO-1 mRNA and protein were induced by the NO donor sodium nitroprusside and 8-bromo-cGMP. The HO-1 mRNA induction by cGMP was prevented by the specific protein kinase G inhibitor KT5823. The cGMP-dependent HO-1 mRNA induction was dose-dependent and transcriptionally regulated, as determined by studies with actinomycin D and a nuclear run-on assay. Cycloheximide lowered the cGMP-dependent induction of HO-1 mRNA to about one half. Luciferase reporter constructs driven by about 800 bp of the 5´-flanking region of the rat HO-1 gene were transiently transfected into primary rat hepatocytes; 8-bromo-cGMP caused a 6-fold induction, which was obliterated by deletion and mutation of the cAMP response element/activator protein-1 (CRE/AP-1) (-665/-654) site. Thus HO-1 induction by cGMP appears to be stimulated by the protein kinase G pathway and may be mediated mainly via a CRE/AP-1 element in the rat HO-1 promoter.
Temperature-induced conformational changes in prosomatostatin-II: implications for processing
Authors: MITRA Joydeep , TANG Xue-jun , ALMO Steven C. , SHIELDS Dennis 
Published: August 2015

Somatostatin (SRIF) is a 14-residue peptide hormone synthesized in the hypothalamus and pancreatic islets. SRIF-14 and an N-terminally extended form, SRIF-28, are generated by the proteolytic processing of an approx. 102-residue precursor prosomatostatin (proSRIF) at a single set of paired basic residues (Arg-Lys) and at a monobasic (Arg) site respectively. Previous work in our laboratory demonstrated that the propeptide of SRIF mediates intracellular sorting; we suggested that this information resides in the prohormone structure. To identify putative sorting domains we have investigated structural features of recombinant anglerfish proSRIF-II purified from Escherichia coli. Two species of proSRIF-II were obtained: a monomeric form and a disulphide-linked dimer. CD analyses revealed that monomeric proSRIF-II lacks appreciable periodic secondary structure; however, on slow heating (2 °C/min) and cooling, it assumed a predominantly α-helical conformation. When subjected to a second heating-and-cooling cycle, the α-helical conformation was maintained. In contrast, the dimeric form of proSRIF-II was predominantly α-helical and its helicity did not increase in response to heating and recooling. Our results suggest that proSRIF-II might exist in several different folding intermediate states.
Muscle-specific mRNA isoform encodes a protein composed mainly of the N-terminal 175 residues of type 2 Ins(1,4,5)P3 receptor
Authors: FUTATSUGI Akira , KUWAJIMA Goro , MIKOSHIBA Katsuhiko 
Published: August 2015

We have found a novel isoform of the mouse type 2 Ins(1,4,5)P3 receptor [Ins(1,4,5)P3R] mRNA by reverse transcriptase-mediated PCR analysis. The novel isoform, which was expressed specifically in skeletal muscle and heart, was generated by the inclusion of a novel exon. As this exon contains a stop codon, the isoform encodes a putative protein (designated TIPR) consisting of 175 acid residues of the type 2 Ins(1,4,5)P3R and the following six residues derived from this exon. We transfected the cDNA of this isoform into COS-7 cells; these cells expressed a 24 kDa protein that was recognized by an antibody against TIPR produced in Escherichia coli. The isoform encoding TIPR was also found in human skeletal muscle and heart. The N-terminal region of Ins(1,4,5)P3R is suggested to have a role in ligand binding and to interact with the C-terminal channel domain of Ins(1,4,5)P3R itself. TIPR might regulate the Ins(1,4,5)P3 signal pathway in both muscles.
Plant mitochondrial pyruvate dehydrogenase complex: purification and identification of catalytic components in potato
Authors: MILLAR A. Harvey , KNORPP Carina , LEAVER Christopher J. , HILL Steven A. 
Published: August 2015

The pyruvate dehydrogenase complex (mPDC) from potato (Solanum tuberosum cv. Romano) tuber mitochondria was purified 40-fold to a specific activity of 5.60 µmol/min per mg of protein. The activity of the complex depended on pyruvate, divalent cations, NAD+ and CoA and was competitively inhibited by both NADH and acetyl-CoA. SDS/PAGE revealed the complex consisted of seven polypeptide bands with apparent molecular masses of 78, 60, 58, 55, 43, 41 and 37 kDa. N-terminal sequencing revealed that the 78 kDa protein was dihydrolipoamide transacetylase (E2), the 58 kDa protein was dihydrolipoamide dehydrogenase (E3), the 43 and 41 kDa proteins were α subunits of pyruvate dehydrogenase, and the 37 kDa protein was the β subunit of pyruvate dehydrogenase. N-terminal sequencing of the 55 kDa protein band yielded two protein sequences: one was another E3; the other was similar to the sequence of E2 from plant and yeast sources but was distinctly different from the sequence of the 78 kDa protein. Incubation of the mPDC with [2-14C]pyruvate resulted in the acetylation of both the 78 and 55 kDa proteins.
Mutant DNA polymerase δ from thermosensitive Schizosaccharomyces pombe strains display reduced stimulation by proliferating cell nuclear antigen
Authors: PERDERISET Mylène , MAGA Giovanni , PIARD Karine , FRANCESCONI Stefania , TRATNER Isabelle , HÜBSCHER Ulrich , BALDACCI Giuseppe 
Published: August 2015

We have isolated and characterized DNA polymerase δ (pol δ) from two thermosensitive Schizosaccharomyces pombe strains, polδts1 and polδts3, mutated in two different evolutionarily conserved domains of the catalytic subunit. At the restrictive temperature of 37 °C polδts1 and polδts3 mutant strains arrest growth in the S phase of the cell cycle. We show that at low levels of primer ends, in vitro stimulation by proliferating cell nuclear antigen (PCNA) of mutant enzymes is lower than stimulation of wild-type pol δ. Affinity for primer (3´-OH) ends and processivity of mutant enzymes do not appear different from wild-type pol δ. In contrast, Vmax values are lower than the wild-type value. The major in vitro defect appears to be decreased stimulation of mutant enzymes by PCNA, resulting in reduced velocity of DNA synthesis. In addition, ts1 pol δ is not stimulated by low PCNA concentration at 37 °C, although low concentrations stimulate activity at 25 °C, suggesting that this thermolability at low levels of primer ends could be its critical defect in vivo. Thus, both ts1 and ts3 pol δ mutations are located in regions of the catalytic subunit that seem necessary, directly or indirectly, for its efficient interaction with PCNA.
Inhibition of the intrinsic NAD+ glycohydrolase activity of CD38 by carbocyclic NAD analogues
Authors: WALL Katherine A. , KLIS Mariola , KORNET John , COYLE Donna , AMÉ Jean-Christophe , JACOBSON Myron K. , SLAMA James T. 
Published: August 2015

Carba-NAD and pseudocarba-NAD are carbocyclic analogues of NAD+ in which a 2,3-dihydroxycyclopentane methanol replaces the β-d-ribonucleotide ring of the nicotinamide riboside moiety of NAD+ [Slama and Simmons (1988) Biochemistry 27, 183–193]. These carbocyclic NAD+ analogues, related to each other as diastereomers, have been tested as inhibitors of the intrinsic NAD+ glycohydrolase activity of human CD38, dog spleen NAD+ glycohydrolase, mouse CD38 and Aplysia californicacADP-ribose synthetase. Pseudocarba-NAD, the carbocyclic dinucleotide in which l-2,3-dihydroxycyclopentane methanol replaces the d-ribose of the nicotinamide riboside moiety of NAD+, was found to be the more potent inhibitor. Pseudocarba-NAD was shown to inhibit the intrinsic NAD+ glycohydrolase activity of human CD38 competitively, with Ki = 148 µM determined for the recombinant extracellular protein domain and Ki = 180 µM determined for the native protein expressed as a cell-surface enzyme on cultured Jurkat cells. Pseudocarba-NAD was shown to be a non-competitive inhibitor of the purified dog spleen NAD+ glycohydrolase, with Kis = 47 µM and Kii = 198 µM. Neither pseudocarba-NAD nor carba-NAD inhibited mouse CD38 or Aplysia californicacADP-ribose synthetase significantly at concentrations up to 1 mM. The results underscore significant species differences in the sensitivity of these enzymes to inhibition, and indicate that pseudocarba-NAD will be useful as an inhibitor of the enzymic activity of human but not mouse CD38 in studies using cultured cells.
Characterization of the human proline/arginine-rich end leucine-rich repeat protein (PRELP) gene promoter and identification of a repressor element
Authors: GROVER Judy , ROUGHLEY Peter J. 
Published: August 2015

The 5´-flanking region of the human proline/arginine-rich end leucine-rich repeat protein (PRELP) gene has been characterized for both promoter and repressor activity by using a variety of reporter gene constructs and transient transfection into chondrocytes or fibroblasts. The human PRELP gene lacks a TATA box, and in its absence a Sp1-binding site residing 29 bp upstream of the transcription start site is essential for initiating gene expression. In contrast, an Ets-binding site residing 497 bp upstream of the transcription start site can lead to the repression of gene expression. The analysis of nuclear proteins by gel retardation studies with the repressor element identified a common protein, presumably an Ets family member, present in neonatal chondrocytes and skin fibroblasts that do not express the PRELP gene. The factor was not detected in nuclear protein preparations from adult chondrocytes in which the PRELP gene is expressed.
A dimeric form of prothrombin on membrane surfaces
Authors: ANDERSON Peter J. 
Published: August 2015

Blood coagulation requires the conversion of zymogens to active enzymes. These reactions are facilitated by Ca2+-dependent protein binding to membrane surfaces containing anionic phospholipids. Here it is shown that only in the presence of both Ca2+ and phospholipid vesicles composed of phosphatidylcholine and phosphatidylserine can a prothrombin dimer be chemically cross-linked. A cross-linker containing evenly spaced reactive groups was prepared by activating the carboxy groups of a ten-residue glutamic acid peptide and allowed to react with physiological concentrations of prothrombin. When Ca2+ and anionic phospholipids were both present during exposure to the cross-linker, it was found that more than 50% of the prothrombin was trapped as a chemically defined dimer with reaction times of the order of 1 min. The dimer yield remained high even when reactions were performed at high phospholipid-to-protein ratios at protein concentrations an order of magnitude less than physiological. Amino acid sequencing of a CNBr peptide produced from the purified dimer localized the cross-link to residues Lys341 and Lys427 of prothrombin. The specificity and high yield under mild conditions of the cross-linking suggest that dimeric membrane bound prothrombin might be a physiologically relevant substrate for the formation of thrombin. Prothrombinase converts this modified protein to an enzyme that catalyses the hydrolysis of a thrombin chromogenic substrate as efficiently as thrombin and is inhibited by a thrombin active-site directed inhibitor, but is a thrombin dimer. The thrombin dimer has impaired activity compared with thrombin with respect to physiological functions requiring binding to exosite I. A model based on the known structure of thrombin is presented that can account for the prothrombin dimer and the properties of the dimeric thrombin formed from it.
Oligosaccharides in molecular recognition
Authors: FEIZI TEN 
Published: August 2015

Summary
The development, organization and growth of complex organisms as well as their interactions with the environment involve an intricate array of molecular recognition events. There is an increased awareness of the involvement of oligosaccharides in many of these processes. In this article, studies of oligosaccharide antigenicity, and the way these have been interpreted with respect to oligosaccharide function will be discussed. In addition, examples of oligosaccharides as receptor, first, as receptors and determinants of susceptibility to an exogenous infective agent and secondly, as recognition structures possibly involved in endogenous interactions, will be described. This will be followed by a discussion of the recent hypothesis in which oligosaccharides arc envisaged as recognition structures and integral components of cell growth-regulating networks. Finally, an outline of new strategies for decoding the information content in glycoprotein oligosaccharides will be given.