bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein identification in cerebrospinal fluid using packed capillary liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry
Authors: Ramström Margareta , Palmblad Magnus , Markides Karin E. , Håkansson Per , Bergquist Jonas 
Published: February 2003

AbstractThe identification and characterization of proteins in complex biological samples such as body fluids, require powerful and reliable tools. Mass spectrometry is today one of the most important methods in such research. This paper reports on the results from the first experiment where a tryptic digest of cerebrospinal fluid was analyzed applying reversed phase liquid chromatography coupled on‐line to a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer. In total, 70 204 peaks were detected, which originated from 16 296 isotopic clusters corresponding to 6551 unique peptide masses. From these masses, 39 proteins were identified in the sample. The amount of sample required for one experiment corresponds to 32 μL of cerebrospinal fluid.
Protein expression profiling of glutathione S‐transferase pi null mice as a strategy to identify potential markers of resistance to paracetamol‐induced toxicity in the liver
Authors: Kitteringham Neil R. , Powell Helen , Jenkins Rosalind E. , Hamlett Jane , Lovatt Cerys , Elsby Robert , Henderson Colin J. , Wolf C. Roland , Pennington Stephen R. , Park B. Kevin 
Published: February 2003

AbstractGST pi (GSTP) is a member of the glutathione S‐transferase (EC 2.5.1.18; GST) family of enzymes that catalyse the conjugation of electrophilic species with reduced glutathione and thus play an important role in the detoxification of electrophilic metabolites. Deletion of GSTP in mice has previously been shown to lead to enhanced susceptibility to chemical‐induced skin carcinoma, consistent with its known metabolic functions. A decreased susceptibility to paracetamol hepatotoxicity has also been observed, which has not been fully explained. One possibility is that deletion of the GSTP gene locus results in compensatory changes in other proteins involved in defence against chemical stress. We have therefore used complementary protein expression profiling techniques to perform a systematic comparison of the protein expression profiles of livers from GSTP null and wild‐type mice. Analysis of liver proteins by two‐dimensional electrophoresis confirmed the absence of GSTP in null mice whereas GSTP represented 3–5% of soluble protein in livers from wild‐type animals. There was a high degree of quantitative and qualitative similarity in other liver proteins between GSTP null and wild‐type mice. There was no evidence that the absence of GSTP in null animals resulted in enhanced expression of other GST isoforms in the null mice (GST alpha, 1.48%, GST mu, 1.68% of resolved proteins) compared with the wild‐type animals (GST alpha, 1.50%, GST mu, 1.40%). In contrast, some members of the thiol specific antioxidant family of proteins, notably antioxidant protein 2 and thioredoxin peroxidases, were expressed at a higher level in the GSTP null mouse livers. These changes presumably reflect the recently described role of GSTP in cell signalling and may underlie the protection against paracetamol toxicity seen in these animals.
Hyperubiquitination of proteins in dilated cardiomyopathy
Authors: Weekes John , Morrison Karen , Mullen Anthony , Wait Robin , Barton Paul , Dunn Michael J. 
Published: February 2003

AbstractProtein degradation by the ubiquitin‐proteasome pathway plays an important role in a variety of fundamental cellular processes, including cell cycle regulation, transcription, antigen processing and muscle remodelling. Research into disorders associated with the ubiquitin‐proteasome system has been mainly in the field of neurodegenerative diseases. It is however becoming increasingly apparent that defects in the system are responsible for a number of non‐neurological pathologies. Based on initial observations made as part of a proteomic analysis of an animal model of dilated cardiomyopathy (DCM) which indicated increased activity of the ubiquitin‐proteasome system, we sought to determine whether this system was perturbed in hearts of human DCM patients. We studied explanted hearts from 12 DCM, 9 ischaemic (IHD) and 12 unused donor hearts. Protein expression was examined using two‐dimensional polyacrylamide gel electrophoresis, Western blotting and immunohistochemistry. Expression of mRNA was examined using real‐time quantitative polymerase chain reaction. Ubiquitinated proteins were affinity purified using a ubiquitin‐binding column and identified using peptide mass fingerprinting. All DCM hearts showed significantly higher expression of certain key enzymes of the ubiquitin‐proteasome pathway. mRNA expression of ubiquitin carboxyl‐terminal hydrolase (UCH) was significantly higher (5.4‐fold) in DCM hearts than in control hearts. Myocytes in sections from DCM hearts stained positively for UCH, whereas control hearts were negative. Overall protein ubiquitination was increased two‐fold in DCM relative to IHD hearts and five‐fold relative to donor hearts. The ubiquitination of a number of distinct proteins was greatly enhanced in DCM hearts as revealed by anti‐ubiquitin Western blots. A number of these proteins were identified using affinity purification and matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry.
Novel subunits of the TATA binding protein free TAFII‐containing transcription complex identified by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry following one‐dimensional gel electrophoresis
Authors: Cavusoglu Nükhet , Brand Marjorie , Tora Laszlo , Van Dorsselaer Alain 
Published: February 2003

AbstractInitiation of transcription of protein‐encoding genes by RNA polymerase II was thought to require the transcription factor II D (TFIID), a complex comprising the TATA binding protein (TBP) and TBP‐associated factors. However, another multiprotein complex isolated more recently and called TFTC (TBP‐free TAFII containing complex), was shown to mediate initiation of RNA polymerase II (Pol II) transcription in the absence of TFIID as well as specific acetylation of histone H3 in a nucleosomal context. Several subunits of the TFTC complex were already identified using classical methods such as Edman based microsequencing and Western blot analysis. In this article we present a mass spectrometry based proteomic approach to confirm previous results and to identify other possible subunits of the TFTC complex. The TFTC complex was separated on one‐dimensional sodium dodecyl sulfate polyacrylamide electrophoresis and analysed by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry and peptide mass fingerprinting. Identifications were realized after databank searches. This new characterization of TFTC complex confirmed the presence of already described subunits (TRRAP, GCN5, SAP130/KIA0017, TAFII150, TAFII135, TAFII100, TAFII80, TAFII20, SPT3 and PAF65β). Moreover, a good coverage of these sequences was obtained. Interestingly, TAFII32 and PAF6α were also determined as potential novel subunits of TFTC. These results together show the suitability and the great potential of this method and offer new perspectives in fundamental studies of transcription factor complexes.
Proteome analysis of the plant pathogen Xylella fastidiosa reveals major cellular and extracellular proteins and a peculiar codon bias distribution
Authors: Smolka Marcus Bustamante , Martins Daniel , Winck Flavia Vischi , Santoro Carlos Eduardo , Castellari Rafael Ramos , Ferrari Fernanda , Brum Itaraju Junior , Galembeck Eduardo , Della Coletta Filho Helvécio , Machado Marcos Antonio , Marangoni Sergio , Novello Jose Camillo 
Published: February 2003

AbstractThe bacteria Xylella fastidiosa is the causative agent of a number of economically important crop diseases, including citrus variegated chlorosis. Although its complete genome is already sequenced, X. fastidiosa is very poorly characterized by biochemical approaches at the protein level. In an initial effort to characterize protein expression in X. fastidiosa we used one‐ and two‐dimensional gel electrophoresis and mass spectrometry to identify the products of 142 genes present in a whole cell extract and in an extracellular fraction of the citrus isolated strain 9a5c. Of particular interest for the study of pathogenesis are adhesion and secreted proteins. Homologs to proteins from three different adhesion systems (type IV fimbriae, mrk pili and hsf surface fibrils) were found to be coexpressed, the last two being detected only as multimeric complexes in the high molecular weight region of one‐dimensional electrophoresis gels. Using a procedure to extract secreted proteins as well as proteins weakly attached to the cell surface we identified 30 different proteins including toxins, adhesion related proteins, antioxidant enzymes, different types of proteases and 16 hypothetical proteins. These data suggest that the intercellular space of X. fastidiosa colonies is a multifunctional microenvironment containing proteins related to in vivo bacterial survival and pathogenesis. A codon usage analysis of the most expressed proteins from the whole cell extract revealed a low biased distribution, which we propose is related to the slow growing nature of X. fastidiosa. A database of the X. fastidiosa proteome was developed and can be accessed via the internet (URL: www.proteome.ibi.unicamp.br).
Synthetic peptides mimicking the interleukin‐6/gp 130 interaction: a two‐helix bundle system. Design and conformational studies
Authors: Zaccaro Laura , Bucci Enrico , Vitale Rosa Maria , Perretta Giuseppe , Fattorusso Roberto , Benedetti Ettore , Saviano Michele , Pedone Carlo 
Published: February 2003

AbstractThe objective of our study was to mimic in a typical reductionist approach the molecular interactions observed at the interface between the gp 130 receptor and interleukin‐6 during formation of their complex. A peptide system obtained by reproducing some of the interleukin‐6/gp 130 molecular interactions into a two‐helix bundle structure was investigated. The solution conformational features of this system were determined by CD and NMR techniques. The CD titration experiments demonstrated that the interaction between the designed peptides is specific and based on a well‐defined stoichiometry. The NMR data confirmed some of the structural features of the binding mechanism as predicted by the rational design and indicated that under our conditions the recognition specificity and affinity can be explained by the formation of a two‐helix bundle. Thus, the data reported herein represent a promising indication on how to develop new peptides able to interfere with formation of the interleukin‐6/gp 130 complex. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Oligopeptide‐mediated helix stabilization of model peptides in aqueous solution
Authors: Maeda Yoshitaka , Nakagawa Terumichi , Kuroda Yoshihiro 
Published: February 2003

AbstractOligopeptide‐mediated helix stabilization of peptides in hydrophobic solutions was previously found by NMR and CD spectroscopic studies. The oligopeptide included the hydrophobic amino acids found in its parent peptide and were interposed by relevant basic or acidic amino acids. The strength of the interactions depended on the amino acid sequences. However, no helix‐stabilizing effect was seen for the peptides in phosphate buffer solution, because the peptides assumed a random‐coil structure. In order to ascertain whether the helix‐stabilizing effect of an oligopeptide on its parent peptide could operate in aqueous solution, model peptides EK17 (Ac‐AEAAAAEAAAKAAAAKA‐NH2) and IFM17 (Ac‐AEAAAAEIFMKAAAAKA‐NH2) that may assume an α‐helix in aqueous solutions were synthesized. Interactions were examined between various oligopeptides (EAAAK, KAAAE, EIFMK, KIFME, KIFMK and EYYEE) and EK17 or IFM17 in phosphate buffer and in 80% trifluoroethanol (TFE)–20% H2O solutions by CD spectra. EAAAK had little effect on the secondary structures of EK17 in both buffer and TFE solutions, while KAAAE, which has the reverse amino acid sequence of EAAAK, had a marked helix‐destabilizing effect on EK17 in TFE. EIFMK and KIFME were found to stabilize the α‐helical structure of EK17 in phosphate buffer solutions, whereas KIFMK and EYYEE destabilized the α‐helical structure of EK17. EIFMK and KIFME had no effect on IFM17, because unexpectedly, IFM17 had appreciable amounts of β‐sheet structure in buffer solution. It was concluded that in order for the helix‐stabilizing effects to operate effectively, the following factors should be satisfied: (1) the model peptide, the α‐helical conformation of which is to be stabilized, should essentially assume an α‐helical structure by nature, and (2) the hydrophobicity of the side‐chains of the oligopeptide should be high enough for the oligopeptide to perform stable specific side chain–side chain intermolecular hydrophobic interactions with the model peptide. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Isolation of Vulgin, a New Antifungal Polypeptide with Mitogenic Activity from the Pinto Bean
Authors: Ye X. Y. , Ng T. B. 
Published: February 2003

AbstractAn antifungal polypeptide bearing an N‐terminal sequence with some homology to chitinases was purified from an extract of pinto beans. The polypeptide, designated vulgin, exerted antifungal activity toward Mycosphaerella arachidicola, Coprinus comatus, Fusarium oxysporum and Botrytis cinerea. Vulgin inhibited translation in a rabbit reticulocyte lysate system with an IC50 of 4.3 µM and HIV‐1 reverse transcriptase activity with an IC50 of 58 µM. Vulgin stimulated in vitro incorporation of methyl [3H] thymidine into mouse splenocytes. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Purification and characterization of a new ribonuclease from fruiting bodies of the oyster mushroom Pleurotus ostreatus
Authors: Ye X. Y. , Ng T. B. 
Published: February 2003

AbstractA ribonuclease (RNase), possessing an N‐terminal sequence disparate from those of ribonucleases from other mushrooms and previously isolated Pleurotus ostreatus RNases, was purified from the fruiting bodies of the edible mushroom Pleurotus ostreatus. The N‐terminal sequence of Pleurotus ostreatus RNase did not manifest homology even to a previously reported RNase from the same mushroom. The ribonuclease was adsorbed on CM‐Sepharose and Mono S. It exhibited a molecular mass of 12 kDa in both sodium dodecyl sulphate‐polyacrylamide gel electrophoresis and gel filtration on Superdex 75. The ribonuclease displayed an activity of 11 490 U/mg on yeast tRNA. The highest ribonuclease activity was exhibited toward poly U, followed by poly A and poly C. No activity was shown toward poly G. The optimal pH for its activity was 7 and the optimal temperature was 55°C. It inhibited cell‐free translation in a rabbit reticulocyte lysate with an IC50 of 240 nM. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Synthesis and circular dichroism study of the human salivary proline‐rich protein IB7
Authors: Simon Cécile , Pianet Isabelle , Dufourc Erick J. 
Published: February 2003

AbstractThe solid phase synthesis of a 59 amino acid human salivary protein IB7 has been accomplished using Fmoc strategy. Because the protein contains 25 proline, 13 glycine and 9 glutamine residues the coupling time, piperidine delivery and acetic anhydride reaction time were increased. Yield after HPLC purification was 35%. Circular dichroism studies revealed that about one third of IB7 residues adopted a type II helix secondary structure, as found in collagen helices. The rest of the sequence adopts a random coil secondary structure. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Surface plasmon resonance spectroscopy in the study of membrane‐mediated cell signalling
Authors: Mozsolits Henriette , Thomas Walter G. , Aguilar Marie‐Isabel 
Published: February 2003

AbstractPeptide–membrane interactions contribute to many important biological processes such as cellular signalling, protein trafficking and ion‐channel formation. During receptor‐mediated signalling, activated intracellular signalling molecules are often recruited into receptor‐induced signalling complexes at the cytoplasmic surface of the cell membrane. Such recruitment can depend upon protein–protein and protein–lipid interactions as well as protein acylation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study these interactions and have provided important information on the relationship between the structure of these proteins involved in cell signalling and their biological function. More recently, surface plasmon resonance (SPR) spectroscopy has also been applied to the study of biomembrane‐based systems using both planar mono‐ or bilayers or liposomes. This article provides an overview of these recent applications, which demonstrate the potential of SPR to enhance our molecular understanding of membrane‐mediated cellular signalling. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Covalent structure and some pharmacological features of native and cleaved α‐KTx12−1, a four disulfide‐bridged toxin from Tityus serrulatus venom
Authors: Pimenta A. M. C. , Mansuelle P. , Diniz C. R. , Martin‐Eauclaire M. F. 
Published: February 2003

AbstractA toxin with four disulfide bridges from Tityus serrulatus venom was able to compete with 125I‐kaliotoxin on rat brain synaptosomal preparations, with an IC50 of 46 nM. The obtained amino acid sequence and molecular mass are identical to the previously described butantoxin. Enzymatic cleavages in the native peptide followed by mass spectrometry peptide mapping analysis were used to determine the disulfide bridge pattern of α‐KTx12−1. Also, after the cleavage of the first six N‐terminal residues, including the unusual disulfide bridge which forms an N‐terminus ring, the potency of the cleaved peptide was found to decrease about 100 fold compared with the native protein. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Evaluation of a soybean product fujiflavone P40 as an antiosteoporotic agent in rats
Authors: Hidaka Saburo , Okamoto Yoshizo , Miyazaki Koji , Uesugi Takehiko 
Published: February 2003

AbstractThe preventive effects of Fujiflavone P40 (a soybean isoflavone product) against both bone loss and periodontal alteration were evaluated using an ovariectomized rat model. Rats were divided into five groups: sham‐operated (Sham), ovariectomized (OVX), OVX given Fujiflavone P40, OVX given 17β‐oestradiol, and OVX given the vehicle for 17β‐oestradiol, respectively. Fujiflavone P40 contains 46.6% isoflavones which consist of 24.1% daidzin, 16.5% glycitin and 5.9% genistin. Administration of Fujiflavone P40 to OVX rats suppressed the body weight gain until 5 weeks. Fujiflavone P40 also decreased total and high‐density lipoprotein (HDL) cholesterols and triglyceride level of OVX rats, significantly. After 7 weeks, Fujiflavone P40 did not recover the coarsened fibre of the periodontal ligament. The ovariectomy decreased the uterine weight by 78%. The administration of 17β ‐oestradiol recovered the weight loss by 99%, while Fujiflavone P40 restored it by 33%. The ovariectomy decreased the tibial bone mineral density (BMD) by 22%. The administration of 17β‐oestradiol to OVX rats recovered the tibial BMD decrease by 100%, while Fujiflavone P40 recovered it by 78%. The results suggest that Fujiflavone P40 may be useful as a preventive agent for osteoporosis. Copyright © 2003 John Wiley & Sons, Ltd.
Anti‐influenza virus activity of crude extract of Ribes nigrum L.
Authors: Knox Yoko M. , Suzutani Tatsuo , Yosida Itsuro , Azuma Masanobu 
Published: February 2003

AbstractThis experiment was designed to detect the antiviral activities of crude fruit extracts of wild Ribes nigrum L. (Kurokarin extract) against influenza virus types A and B. Kurokarin extract was prepared as follows: fruits of Ribes nigrum L. were heated at 50 °C in a heating tank, and then ground under anaerobic conditions. The extracts were centrifuged, and the supernatant fluid was filtered and sterilized by infrared rays. The crude extract was diluted with Eagle's minimum essential medium (MEM) and the solution was adjusted to a pH 7.2 with 0.1 N or 1 N NaOH. Proven anti‐influenza virus effects of the extracts were shown. The concentration of extract required to inhibit the plaque formation of both IVA and IVB by 50% (IC50) was 3.2 μg/mL. Both IVA and IVB were directly inactivated up to 99% by 10 μg/mL of the extract at pH 2.8, and 95% to 98% by this dose at pH 7.2. The growth of IVA in cells treated with 10 and 100 μg/mL of the extract for 6 h after infection was completely suppressed. Virus titres in culture fluids of the cells treated with 100 μg/mL of Kurokarin extract for 1 h at 8 to 9 h after infection, were completely suppressed, indicating that the extract inhibited the virus release from the infected cells. Copyright © 2003 John Wiley & Sons, Ltd.
A new bioactive steroidal saponin from Sansevieria cylindrica
Authors: da Silva Antunes Alexandra , da Silva Bernadete Pereira , Parente José Paz , Valente Ana Paula 
Published: February 2003

AbstractA new steroidal saponin was isolated from the leaves of Sansevieria cylindrica. Its structure was established as (3β,12β,15α,25S)‐26‐(β‐D‐glucopyranosyloxy)‐22‐hydroxyfurost‐5‐en‐3‐yl 12‐O‐ (6‐deoxy‐α‐L‐mannopyranosyl)‐15‐O‐(6‐deoxy‐α‐L‐mannopyranosyl)‐β‐D‐glucopyranoside. The structural identification was performed using detailed analyses of 1H and 13C NMR spectra including 2D NMR spectroscopic techniques (COSY, HETCOR, HMBC and HMQC) and chemical conversions. The steroidal saponin showed no haemolytic effects in the in vitro assays and demonstrated inhibition of the capillary permeability activity. Copyright © 2003 John Wiley & Sons, Ltd.
In vitro antiplasmodial evaluation of medicinal plants from Zimbabwe
Authors: Kraft Carola , Jenett‐Siems Kristina , Siems Karsten , Jakupovic Jasmin , Mavi Steven , Bienzle Ulrich , Eich Eckart 
Published: February 2003

AbstractIn this study the in vitro antiplasmodial activities of extracts from Cussonia spicata (Araliaceae), Artemisia afra, Vernonia colorata, V. natalensis (Asteraceae), Parinari curatellifolia (Chrysobalanaceae), Clutia hirsuta, Flueggea virosa, (Euphorbiaceae), Adenia gummifera (Passifloraceae) and Hymenodictyon floribundum, (Rubiaceae) were evaluated. The lipophilic extracts from the aerial parts of Artemisia afra and Vernonia colorata proved to be the most active against the chloroquine‐sensitive strain PoW and against the chloroquine‐resistant clone Dd2 of Plasmodium falciparum. Bioassay‐guided fractionation of the extract of A. afra yielded seven flavonoids, from which acacetin, genkwanin and 7‐methoxyacacetin showed in vitro activity; the IC50 values ranged from 4.3 μg/mL to 12.6 μg/mL. In addition, several sesquiterpene lactones could be obtained from the most active fractions. Whereas eudesmaafraglaucolide proved to be inactive, the guaianolides 1‐desoxy‐1α‐peroxy‐rupicolin A‐8‐O‐acetate, 1α,4α‐dihydroxybishopsolicepolide and rupicolin A‐8‐O‐acetate revealed in vitro antiplasmodial activity. Evaluation of V. colorata gained four sesquiterpenes 11β,13‐dihydrovernodalin, vernodalol, 11β,13‐dihydrovernolide and 11β,13,17,18‐tetrahydrovernolide, from which the first two constituents exhibited the strongest antiplasmodial activity (IC50 values: 1.1–4.8 μg/mL). Copyright © 2003 John Wiley & Sons, Ltd.