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Peptide Sequence (peptide + sequence)
Kinds of Peptide Sequence Selected AbstractsIdentification of a Peptide Sequence in Albumin that Potentiates Superoxide Production by MicrogliaJOURNAL OF NEUROCHEMISTRY, Issue 6 2000Yoichi Nakamura Abstract: Microglial activation has recently been recognized as acause of damage in various neurodegenerative diseases. A possible mechanismunderlying this damage is the activation of microglia by serum factors leakedthrough a disruption of the blood,brain barrier, which in turn triggermicroglial cell proliferation and the release of various substances toxic toneurons, such as superoxide (O2 - ). We recently reportedthat serum albumin enhanced O2 - producation in culturedrat microglia stimulated by phorbol ester. In the present report, we identifythe active site of this enhancement within the albumin molecule. We purifiedan active subfragment from trypsin-treated bovine serum albumin that wascomposed of 12-mer and 33-mer peptides connected by a disulfide bond. Thechemically synthesized 12-mer peptide showed activity within a concentrationrange (,10 -7M) equivalent to that of albumin. Theactivities of a series of synthesized peptides conclusively indicated that theminimum active sequence was Leu-His-Thr-Leu. The present study may shed lighton the mechanism of neuronal cell damage in various neurodegenerativediseases. [source] Tunable, Temperature-Responsive Polynorbornenes with Side Chains Based on an Elastin Peptide Sequence,ANGEWANDTE CHEMIE, Issue 44 2009Rosemary Zufallscopolymere aus der lebenden Ringöffnungsmetathese-Polymerisation von Norbornenmonomeren, die entweder die VPGVG-Peptidsequenz von Elastin oder einen Pentaethylenglycol-Substituenten enthalten (siehe Schema; Mes=Mesityl, pyr=Pyridin), verfügen über eine untere kritische Entmischungstemperatur (LCST), die leicht durch Variieren des Monomerverhältnisses einstellbar ist. [source] Polyphyletic photosynthetic reaction centre genes in oligotrophic marine GammaproteobacteriaENVIRONMENTAL MICROBIOLOGY, Issue 6 2007Jang-Cheon Cho Summary Ecological studies indicate that aerobic anoxygenic phototrophic bacteria (AAP) that use bacteriochlorophyll to support phototrophic electron transport are widely distributed in the oceans. All cultivated marine AAP are alpha-3 and alpha-4 Proteobacteria, but metagenomic evidence indicates that uncultured AAP Gammaproteobacteria are important members of ocean surface microbial communities. Here we report the description of obligately oligotrophic, marine Gammaproteobacteria that have genes for aerobic anoxygenic photosynthesis. Three strains belonging to the OM60 clade were isolated in autoclaved seawater media. Polymerase chain reaction assays for the pufM gene show that these strains contain photosynthetic reaction centre genes. DNA sequencing and phylogenetic analysis indicate that the pufM genes are polyphyletic, suggesting multiple instances of lateral gene transfer. Peptide sequences from six photosynthesis genes (pufL, pufM, pufC, pufB, pufA and puhA) were detected by proteomic analyses of strain HTCC2080 cells grown aerobically in seawater. They closely match predicted peptides from an environmental seawater bacterial artificial chromosome clone of gammaproteobacterial origin, thus identifying the OM60 clade as a significant source of gammaproteobacterial AAP genes in marine systems. The cell yield and rate of growth of HTCC2080 in autoclaved, aerobic seawater increased in the light. These findings identify the OM60 clade as a source of Gammaproteobacteria AAP genes in coastal oceans, and demonstrate that aerobic, anoxygenic photosynthetic metabolism can enhance the productivity of marine oligotrophic bacteria that also grow heterotrophically in darkness. [source] Selective enhancement of the activity of C-terminally truncated, but not intact, acetylcholinesteraseJOURNAL OF NEUROCHEMISTRY, Issue 1 2008Martina Zimmermann Abstract Acetylcholinesterase (AChE) is one of the fastest enzymes approaching the catalytic limit of enzyme activity. The enzyme is involved in the terminal breakdown of the neurotransmitter acetylcholine, but non-enzymatic roles have also been described for the entire AChE molecule and its isolated C-terminal sequences. These non-cholinergic functions have been attributed to both the developmental and degenerative situation: the major form of AChE present in these conditions is monomeric. Moreover, AChE has been shown to lose its typical characteristic of substrate inhibition in both development and degeneration. This study characterizes a form of AChE truncated after amino acid 548 (T548-AChE), whose truncation site is homologue to that of a physiological form of T-AChE detected in fetal bovine serum that has lost its C-terminal moiety supposedly due to proteolytic cleavage. Peptide sequences covered by this C-terminal sequence have been shown to be crucially involved in both developmental and degenerative mechanisms in vitro. Numerous studies have addressed the structure,function relationship of the AChE C-terminus with T548-AChE representing one of the most frequently studied forms of truncated AChE. In this study, we provide new insight into the understanding of the functional characteristics that T548-AChE acquires in solution: T548-AChE is incubated with agents of varying net charge and molecular weight. Together with kinetic studies and an analysis of different molecular forms and aggregation states of T548-AChE, we show that the enzymatic activity of T548-AChE, an enzyme verging at its catalytic limit is, nonetheless, apparently enhanced by up to 800%. We demonstrate, first, how the activity of T548-AChE can be enhanced through agents that contain highly positive charged moieties. Moreover, the un-competitive mechanism of activity enhancement most likely involves the peripheral anionic site of AChE that is reflected in delayed substrate inhibition being observed for activity enhanced T548-AChE. The data provides evidence towards a mechanistic and functional link between the form of AChE unique to both development and degeneration and a C-terminal peptide of T-AChE acting under those conditions. [source] Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approachPROTEIN SCIENCE, Issue 3 2001Emine Cavdar Koc Abstract Proteins in the small subunit of the mammalian mitochondrial ribosome were separated by two-dimensional polyacrylamide gel electrophoresis. Four individual proteins were subjected to in-gel Endoprotease Lys-C digestion. The sequences of selected proteolytic peptides were obtained by electrospray tandem mass spectrometry. Peptide sequences obtained from in-gel digestion of individual spots were used to screen human, mouse, and rat expressed sequence tag databases, and complete consensus cDNAs for these species were deduced in silico. The corresponding protein sequences were characterized by comparison to known ribosomal proteins in protein databases. Four different classes of mammalian mitochondrial small subunit ribosomal proteins were identified. Only two of these proteins have significant sequence similarities to ribosomal proteins from prokaryotes. These proteins are homologs to Escherichia coli S9 and S5 proteins. The presence of these newly identified mitochondrial ribosomal proteins are also investigated in the Drosophila melanogaster, Caenorhabditis elegans, and in the genomes of several fungi. [source] Selective targeting of a laccase from Stachybotrys chartarum covalently linked to a carotenoid-binding peptideCHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2004G.G. Janssen Abstract:, A two-step targeting strategy was used to identify improved laccases for bleaching carotenoid-containing stains on fabric. We first applied a modified phage display technique to identify peptide sequences capable of binding specifically to carotenoid stains and not to fabric. Prior deselection on the support on which the carotenoid was localized, increased stringency during the biopanning target selection process, and analysis of the phage peptides' binding to the target after acid elution and polymerase chain reaction (PCR) postacid elution, were used to isolate phage peptide libraries with increased binding selectivity and affinity. Peptide sequences were selected based on identified consensus motifs. We verified the enhanced carotenoid-binding properties of the peptide YGYLPSR and subsequently cloned and expressed C-terminal variants of laccase from Stachybotrys chartarum containing carotenoid-binding peptides YGYLPSR, IERSAPATAPPP, KASAPAL, CKASAPALC, and SLLNATK. These targeted peptide,laccase fusions demonstrate enhanced catalytic properties on stained fabrics. [source] Microwave-Assisted Paal,Knorr Reaction , Three-Step Regiocontrolled Synthesis of Polysubstituted Furans, Pyrroles and ThiophenesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2005Giacomo Minetto Abstract An efficient and highly versatile synthesis of furans, pyrroles and thiophenes is described. Starting from commercially available or easily prepared ,-keto esters, functional homologation provides differently substituted 1,4-diketones that can be transformed, through a microwave-assisted Paal,Knorr condensation, into the corresponding methoxycarbonyl heterocycles. The methoxycarbonyl moiety can be directly transformed into an NH2 group by hydrolysis to carboxylic acid and Curtius rearrangement or into an amide by reaction with a primary amine in the presence of Me3Al. The method is compatible with the presence of a CbzNH group so that the final heterocycle can be inserted into a peptide sequence as a turn inducer. By using this procedure, a collection of more than 60 different tetrasubstitued pyrroles or trisubstituted thiophenes has been prepared. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Evolution of a novel function: nutritive milk in the viviparous cockroach, Diploptera punctataEVOLUTION AND DEVELOPMENT, Issue 2 2004Anna Williford Summary Cockroach species show different degrees of maternal contribution to the developing offspring. In this study, we identify a multigene family that encodes water-soluble proteins that are a major component of nutritive "Milk" in the cockroach, Diploptera punctata. This gene family is associated with the evolution of a new trait, viviparity, in which the offspring receive nutrition during the gestation period. Twenty-five distinct Milk complementary DNAs were cloned and partially characterized. These complementary DNAs encode 22 distinct Milk peptides, each of length 171 amino acids, including a 16-amino acid signal peptide sequence. Southern blot analysis confirms the presence of multiple copies of Milk genes in D. punctata. Northern analysis indicates tissue- and stage-specific Milk gene expression. Examination of the deduced amino acid sequences identifies the presence of structurally conserved regions diagnostic of the lipocalin protein family. The shared exon/intron structure of one of the Milk loci with lipocalin genes further supports a close evolutionary relationship between these sequences. [source] Interaction with calmodulin is important for the secretion of thimet oligopeptidase following stimulationFEBS JOURNAL, Issue 16 2009Lilian C. Russo Thimet oligopeptidase (EC 3.4.24.15; EP24.15) was originally described as a neuropeptide-metabolizing enzyme, highly expressed in the brain, kidneys and neuroendocrine tissue. EP24.15 lacks a typical signal peptide sequence for entry into the secretory pathway and is secreted by cells via an unconventional and unknown mechanism. In this study, we identified a novel calcium-dependent interaction between EP24.15 and calmodulin, which is important for the stimulated, but not constitutive, secretion of EP24.15. We demonstrated that, in vitro, EP24.15 and calmodulin physically interact only in the presence of Ca2+, with an estimated Kd value of 0.52 ,m. Confocal microscopy confirmed that EP24.15 colocalizes with calmodulin in the cytosol of resting HEK293 cells. This colocalization markedly increases when cells are treated with either the calcium ionophore A23187 or the protein kinase A activator forskolin. Overexpression of calmodulin in HEK293 cells is sufficient to greatly increase the A23187-stimulated secretion of EP24.15, which can be inhibited by the calmodulin inhibitor calmidazolium. The specific inhibition of protein kinase A with KT5720 reduces the A23187-stimulated secretion of EP24.15 and inhibits the synergistic effects of forskolin with A23187. Treatment with calmidazolium and KT5720 nearly abolishes the stimulatory effects of A23187 on EP24.15 secretion. Together, these data suggest that the interaction between EP24.15 and calmodulin is regulated within cells and is important for the stimulated secretion of EP24.15 from HEK293 cells. Structured digital abstract ,,MINT-7148420: EP24.15 (uniprotkb:P52888) and Calmodulin (uniprotkb:P62161) bind (MI:0407) by surface plasmon resonance (MI:0107) ,,MINT-7148437: EP24.15 (uniprotkb:P52888) and Calmodulin (uniprotkb:P62158) colocalize (MI:0403) by surface plasmon resonance (MI:0107) ,,MINT-7148406: Calmodulin (uniprotkb:P62161) binds (MI:0407) to EP24.15 (uniprotkb:P52888) by pull down (MI:0096) [source] Mass spectrometric characterization of the covalent modification of the nitrogenase Fe-protein in Azoarcus sp.FEBS JOURNAL, Issue 13 2009Nitrogenase Fe-protein modification was analyzed in the endophytic ,-proteobacterium Azoarcus sp. BH72. Application of modern MS techniques localized the modification in the peptide sequence and revealed it to be an ADP-ribosylation on Arg102 of one subunit of nitrogenase Fe-protein. A double digest with trypsin and endoproteinase Asp-N was necessary to obtain an analyzable peptide because the modification blocked the trypsin cleavage site at this residue. Furthermore, a peptide extraction protocol without trifluoroacetic acid was crucial to acquire the modified peptide, indicating an acid lability of the ADP-ribosylation. This finding was supported by the presence of a truncated version of the original peptide with Arg102 exchanged by ornithine. Site-directed mutagenesis verified that the ADP-ribosylation occurred on Arg102. With our approach, we were able to localize a labile modification within a large peptide of 31 amino acid residues. The present study provides a method suitable for the identification of so far unknown protein modifications on nitrogenases or other proteins. It represents a new tool for the MS analysis of protein mono-ADP-ribosylations. [source] A 49 kDa microtubule cross-linking protein from Artemia franciscana is a coenzyme A-transferaseFEBS JOURNAL, Issue 24 2003Mindy M. Oulton Embryos and larvae of the brine shrimp, Artemia franciscana, were shown previously to possess a protein, now termed p49, which cross-links microtubules in vitro. Molecular characteristics of p49 were described, but the protein's identity and its role in the cell were not determined. Degenerate oligonucleotide primers designed on the basis of peptide sequence obtained by Edman degradation during this study were used to generate p49 cDNAs by RT-PCR and these were cloned and sequenced. Comparison with archived sequences revealed that the deduced amino acid sequence of p49 resembled the Drosophila gene product CG7920, as well as related proteins encoded in the genomes of Anopheles and Caenorhabditis. Similar proteins exist in several bacteria but no evident homologues were found in vertebrates and plants, and only very distant homologues resided in yeast. When evolutionary relationships were compared, p49 and the homologues from Drosophila, Anopheles and Caenorhabditis formed a distinct subcluster within phylogenetic trees. Additionally, the predicted secondary structures of p49, 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum and glutaconate CoA-transferase from Acidaminococcus fermentans were similar and the enzymes may possess related catalytic mechanisms. The purified Artemia protein exhibited 4-hydroxybutyrate CoA-transferase activity, thereby establishing p49 as the first crustacean CoA-transferase to be characterized. Probing of Western blots with an antibody against p49 revealed a cross-reactive protein in Drosophila that associated with microtubules, but to a lesser extent than did p49 from Artemia. [source] Oosp1 encodes a novel mouse oocyte-secreted proteinGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 3 2001Changning Yan Abstract Summary: Oocyte-somatic cell communication is necessary for normal ovarian function. However, the identities of the majority of oocyte-secreted proteins remain unknown. A novel cDNA encoding mouse oocyte- secreted protein 1 (OOSP1) was identified using a modified subtractive hybridization screen. The Oosp1 cDNA encodes a 202-amino acid protein that contains a 21-amino acid signal peptide sequence, 5 putative N-linked glycosylation consensus sequences, and 6 cysteines that are predicted to form 3 disulfide bonds. OOSP1 shares amino acid identity with placental-specific protein 1 (PLAC1), a secreted protein expressed in the placenta and the ectoplacental cone. The Oosp1 mRNA is approximately 1.0 kb and is present at high levels in the oocytes of adult ovaries and at lower levels in the spleen. The mouse Oosp1 gene is 5 exons, spans greater than 16.4 kb, and localizes to chromosome 19 at a position that shares synteny with human chromosome 11q12,11q13. The identification of OOSP1 as a new oocyte-secreted protein permits future in vitro and in vivo functional analyses to define its role in ovarian folliculogenesis. genesis 31:105,110, 2001. © 2001 Wiley-Liss, Inc. [source] Molecular characterization of the amplified carboxylesterase gene associated with organophosphorus insecticide resistance in the brown planthopper, Nilaparvata lugensINSECT MOLECULAR BIOLOGY, Issue 6 2000Graham J. Small Abstract Widespread resistance to organophosphorus insecticides (OPs) in Nilaparvata lugens is associated with elevation of carboxylesterase activity. A cDNA encoding a carboxylesterase, Nl-EST1, has been isolated from an OP-resistant Sri Lankan strain of N. lugens. The full-length cDNA codes for a 547-amino acid protein with high homology to other esterases/lipases. Nl-EST1 has an N-terminal hydrophobic signal peptide sequence of 24 amino acids which suggests that the mature protein is secreted from cells expressing it. The nucleotide sequence of the homologue of Nl-EST1 in an OP-susceptible, low esterase Sri Lankan strain of N. lugens is identical to Nl-EST1. Southern analysis of genomic DNA from the Sri Lankan OP-resistant and susceptible strains suggests that Nl-EST1 is amplified in the resistant strain. Therefore, resistance to OPs in the Sri Lankan strain is through amplification of a gene identical to that found in the susceptible strain. [source] Novel bioactive scaffolds with fibronectin recognition nanosites based on molecular imprinting technologyJOURNAL OF APPLIED POLYMER SCIENCE, Issue 6 2010Elisabetta Rosellini Abstract Biomimetic materials for application in the field of tissue engineering are usually obtained through covalent bonding between the polymer backbone and the bioactive molecules. A totally new approach, proposed for the first time by our research group, for the creation of advanced synthetic support structures for cell adhesion and proliferation is represented by molecular imprinting (MI) technology. In this article, we describe the synthesis and characterization of molecularly imprinted polymers with recognition properties toward a fibronectin peptide sequence and their application as functionalization structures. Polymers, in the form of densely fused microgel particles, were obtained by precipitation polymerization. The imprinted particles showed good performance in terms of recognition capacity and quantitative rebinding; moreover, the epitope effect was observed, with the particles able to recognize and rebind not only the specific peptide sequence but also a larger fibronectin fragment. The cytotoxicity tests showed normal vitality in C2C12 myoblasts cultured in a medium that was put in contact with the imprinted particles. Therefore, imprinted particles were used to functionalize synthetic polymeric films by deposition on their surface. The deposition of the imprinted particles did not alter their specific recognition and rebinding behavior. The most remarkable result was obtained by the biological characterization: in fact, the functionalized materials appeared able to promote cell adhesion and proliferation. These results are very promising and suggest that MI can be used as an innovative functionalization technique to prepare bioactive scaffolds with an effective capacity for improving tissue regeneration. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010 [source] A Mu-class glutathione S -transferase from gills of the marine shrimp Litopenaeus vannamei: Purification and characterizationJOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 2 2007Carmen A. Contreras-Vergara Abstract Glutathione S -transferases (GSTs) are a family of detoxifying enzymes that catalyze the conjugation of glutathione (GSH) to electrophiles, thereby increasing the solubility of GSH and aiding its excretion from the cell. In this study, a glutatione S -transferase from the gills of the marine shrimp Litopenaeus vannamei was purified by affinity chromatography using a glutathione,agarose affinity column. GST was purified to homogeneity as judged by reducing SDS-PAGE and zymograms. This enzyme is a homodimer composed of ,25-kDa subunits and identified as a Mu-class GST based on its activity against 1-chloro-2,4-dinitrobenzene (CDNB) and internal peptide sequence. The specific activity of purified GST was 440.12 ,mol/(min mg), and the Km values for CDNB and GSH are very similar (390 and 335 ,M, respectively). The intersecting pattern of the initial velocities of this enzyme in the Lineweaver,Burke plot is consistent with a sequential steady-state kinetic mechanism. The high specific activity of shrimp GST may be related to a highly effective detoxification mechanism necessary in gills since they are exposed to the external and frequently contaminated environment. © 2007 Wiley Periodicals, Inc. J Biochem Mol Toxicol 21:62,67, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20162 [source] Protein identification by peptide mass fingerprinting and peptide sequence tagging with alternating scans of nano-liquid chromatography/infrared multiphoton dissociation Fourier transform ion cyclotron resonance mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 12 2003Toshiyuki Kosaka Abstract We have developed a method for protein identification with peptide mass fingerprinting and sequence tagging using nano liquid chromatography (LC)/Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). To achieve greater sensitivity, a nanoelectrospray (nano-ES) needle packed with reversed-phase medium was used and connected to the nano-ES ion source of the FTICR mass spectrometer. To obtain peptide sequence tag information, infrared multiphoton dissociation (IRMPD) was carried out in nano-LC/FTICR-MS analysis. The analysis involves alternating nano-ES/FTICR-MS and nano-ES/IRMPD-FTICR-MS scans during a single LC run, which provides sets of parent and fragment ion masses of the proteolytic digest. The utility of this alternating-scan nano-LC/IRMPD-FTICR-MS approach was evaluated by using bovine serum albumin as a standard protein. We applied this approach to the protein identification of rat liver diacetyl-reducing enzyme. It was demonstrated that this enzyme was correctly identified as 3-,-hydroxysteroid dehydrogenase by the alternating-scan nano-LC/IRMPD-FTICR-MS approach with accurate peptide mass fingerprinting and peptide sequence tagging. Copyright © 2003 John Wiley & Sons, Ltd. [source] Negative and positive ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and positive ion nano-electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus speciesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2001Gerold Bacher Abstract A general approach for the detailed characterization of sodium borohydride-reduced peptidoglycan fragments (syn. muropeptides), produced by muramidase digestion of the purified sacculus isolated from Bacillus subtilis (vegetative cell form of the wild type and a dacA mutant) and Bacillus megaterium (endospore form), is outlined based on UV matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) quadrupole ion trap (QIT) mass spectrometry (MS). After enzymatic digestion and reduction of the resulting muropeptides, the complex glycopeptide mixture was separated and fractionated by reversed-phase high-performance liquid chromatography. Prior to mass spectrometric analysis, the muropeptide samples were subjected to a desalting step and an aliquot was taken for amino acid analysis. Initial molecular mass determination of these peptidoglycan fragments (ranging from monomeric to tetrameric muropeptides) was performed by positive and negative ion MALDI-MS using the thin-layer technique with the matrix ,-cyano-4-hydroxycinnamic acid. The results demonstrated that for the fast molecular mass determination of large sample numbers in the 0.8,10 pmol range and with a mass accuracy of ±0.07%, negative ion MALDI-MS in the linear TOF mode is the method of choice. After this kind of muropeptide screening often a detailed primary structural analysis is required owing to ambiguous data. Structural data could be obtained from peptidoglycan monomers by post-source decay (PSD) fragment ion analysis, but not from dimers or higher oligomers and not with the necessary sensitivity. Multistage collision-induced dissociation (CID) experiments performed on an nESI-QIT instrument were found to be the superior method for structural characterization of not only monomeric but also of dimeric and trimeric muropeptides. Up to MS4 experiments were sometimes necessary to obtain unambiguous structural information. Three examples are presented: (a) CID MSn (n = 2,4) of a peptidoglycan monomer (disaccharide-tripeptide) isolated from B. subtilis (wild type, vegetative cell form), (b) CID MSn (n = 2,4) of a peptidoglycan dimer (bis-disaccharide-tetrapentapeptide) obtained from a B. subtilis mutant (vegetative cell form) and (c) CID MS2 of a peptidoglycan trimer (a linear hexasaccharide with two peptide side chains) isolated from the spore cortex of B. megaterium. All MSn experiments were performed on singly charged precursor ions and the MS2 spectra were dominated by fragments derived from interglycosidic bond cleavages. MS3 and MS4 spectra exhibited mainly peptide moiety fragment ions. In case of the bis-disaccharide-tetrapentapeptide, the peptide branching point could be determined based on MS3 and MS4 spectra. The results demonstrate the utility of nESI-QIT-MS towards the facile determination of the glycan sequence, the peptide linkage and the peptide sequence and branching of purified muropeptides (monomeric up to trimeric forms). The wealth of structural information generated by nESI-QIT-MSn is unsurpassed by any other individual technique. Copyright © 2001 John Wiley & Sons, Ltd. [source] 14-3-3 epsilon modulates the stimulated secretion of endopeptidase 24.15JOURNAL OF NEUROCHEMISTRY, Issue 1 2005Flávia R. Carreño Abstract Endopeptidase 24.15 (ep24.15: EC3.4.24.15), a secreted protein involved in peptide metabolism, is unusual in that it does not contain a signal peptide sequence. In this work, we describe the physical interaction between ep24.15 and 14-3-3 epsilon, one isoform of a family of ubiquitous phosphoserine/threonine-scaffold proteins that organizes cell signaling and is involved in exocytosis. The interaction between ep24.15 and 14-3-3 epsilon increased following phosphorylation of ep24.15 at Ser644 by protein kinase A (PKA). The co-localization of ep24.15 and 14-3-3 epsilon was increased by exposure of HEK293 cells (human embryonic kidney cells) to forskolin (10 µm). Overexpression of 14-3-3 epsilon in HEK293 cells almost doubled the secretion of ep24.15 stimulated by A23187 (7.5 µm) from 10%[1.4 ± 0.24 AFU/(min 106 cells)] to 19%[2.54 ± 0.24 AFU/(min 106 cells)] (p < 0.001) of the total intracellular enzyme activity. Treatment with forskolin had a synergistic effect on the A23187-stimulated secretion of ep24.15 that was totally blocked by the PKA inhibitor KT5720. The ep24.15 point mutation S644A reduced the co-localization of ep24.15 and 14-3-3 in stably transfected HEK293 cells. Indeed, secretion of the ep24.15 S644A mutant from these cells was only slightly stimulated by A23187 and insensitive to forskolin, in contrast to that of the wild type enzyme. Together, these data suggest that prior interaction with 14-3-3 is an important step in the unconventional stimulated secretion of ep24.15. [source] A study to assess the cross-reactivity of cellulose membrane-bound peptides with detection systems: an analysis at the amino acid levelJOURNAL OF PEPTIDE SCIENCE, Issue 6 2010Carsten C. Mahrenholz Abstract The growing demand for binding assays to study protein,protein interaction can be addressed by peptide array-based methods. The SPOT technique is a widespread peptide-array technology, which is able to distinguish semi-quantitatively the binding affinities of peptides to defined protein targets within one array. The quality of an assay system used for probing peptide arrays depends on the well-balanced combination of screening and read-out methods. The former address the steady-state of analyte capture, whereas the latter provide the means to detect captured analyte. In all cases, however, false-positive results can occur when challenging a peptide array with analyte or detecting captured analyte with label conjugates. Little is known about the cross-reactivity of peptides with the detection agents. Here, we describe at the amino acid level the potential of (i) 5-(and 6)-carboxytetramethylrhodamine (5(6)-TAMRA), (ii) fluoresceinisothiocyanate in form of the peptide-bound fluorescein-substituted thiourea derivative (FITC), and (iii) biotin/streptavidin-POD to cross-react with individual amino acids in a peptide sequence. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source] Interaction of S413 -PV cell penetrating peptide with model membranes: relevance to peptide translocation across biological membranesJOURNAL OF PEPTIDE SCIENCE, Issue 5 2007Miguel Mano Abstract Cell penetrating peptides (CPPs) have been successfully used to mediate the intracellular delivery of a wide variety of molecules of pharmacological interest both in vitro and in vivo, although the mechanisms by which the cellular uptake occurs remain unclear and controversial. Following our previous work demonstrating that the cellular uptake of the S413 -PV CPP occurs mainly through an endocytosis-independent mechanism, we performed a detailed biophysical characterization of the interaction of this peptide with model membranes. We demonstrate that the interactions of the S413 -PV peptide with membranes are essentially of electrostatic nature. As a consequence of its interaction with negatively charged model membranes, the S413 -PV peptide becomes buried into the lipid bilayer, which occurs concomitantly with significant peptide conformational changes that are consistent with the formation of a helical structure. Comparative studies using two related peptides demonstrate that the conformational changes and the extent of cell penetration are dependent on the peptide sequence, indicating that the helical structure acquired by the S413 -PV peptide is relevant for its nonendocytic uptake. Overall, our data suggest that the cellular uptake of the S413 -PV CPP is a consequence of its direct translocation through cell membranes, following conformational changes induced by peptide-membrane interactions. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between ,-helical and ,-hairpin conformations mediated by collapsed conformational statesJOURNAL OF PEPTIDE SCIENCE, Issue 5 2007Sunita Patel Abstract The peptide TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase adopts a helical conformation in the crystal structure and is a site for two hydrated helical segments, which are thought to be helical folding intermediates. Overlapping sequences of four to five residues from the peptide, sample both helical and strand conformations in known protein structures, which are dissimilar to glyceraldehyde-3-phosphate dehydrogenase suggesting that the peptide may have a structural ambivalence. Molecular dynamics simulations of the peptide sequence performed for a total simulation time of 1.2 µs, starting from the various initial conformations using GROMOS96 force field under NVT conditions, show that the peptide samples a large number of conformational forms with transitions from ,-helix to ,-hairpin and vice versa. The peptide, therefore, displays a structural ambivalence. The mechanism from ,-helix to ,-hairpin transition and vice versa reveals that the compact bends and turns conformational forms mediate such conformational transitions. These compact structures including helices and hairpins have similar hydrophobic radius of gyration (Rgh) values suggesting that similar hydrophobic interactions govern these conformational forms. The distribution of conformational energies is Gaussian with helix sampling lowest energy followed by the hairpins and coil. The lowest potential energy of the full helix may enable the peptide to take up helical conformation in the crystal structure of the glyceraldehyde-3-phosphate dehydrogenase, even though the peptide has a preference for hairpin too. The relevance of folding and unfolding events observed in our simulations to hydrophobic collapse model of protein folding are discussed. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Post-synthesis incorporation of a lipidic side chain into a peptide on solid supportJOURNAL OF PEPTIDE SCIENCE, Issue 11 2002Céline Douat Abstract A new strategy for the synthesis of lipopeptides has been developed. Using Weinreb (N -methoxy, N -methyl) amide as an aldehyde function precursor on the side chains of Asp or Glu residues, this new strategy avoids the synthesis of a lipidic amino acid residue before its incorporation in the peptide sequence. The aldehyde generated on the solid support can react with ylides leading to unsaturated or saturated side chains or with various nucleophiles to yield non-coded amino acid residues incorporated into the sequence. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis, conformation and biological activity of linear and cyclic Thr6 -bradykinin analogues containing N -benzylglycine in place of phenylalanine,JOURNAL OF PEPTIDE SCIENCE, Issue 12 2001L. Biondi Abstract Three linear Thr6 -bradykinin analogues in which either one or both the two phenylalanine residues in the peptide sequence have been substituted by N -benzylglycine (BzlGly) and their head-to-tail cyclic analogues were synthesized and tested on an isolated rat duodenum preparation. The linear (BzlGly5,Thr6 -BK, BzlGly8,Thr6 -BK and BzlGly5,8,Thr6 -BK) and the cyclic (cyclo BzlGly5,Thr6 -BK, cyclo BzlGly8,Thr6 -BK and cyclo BzlGly5,8,Thr6 -BK) peptoid-like analogues were characterized by amino acid analysis, optical rotation, analytical HPLC and MALDI-TOF mass spectroscopy. The conformational features of both the linear and cyclic derivatives were investigated by FT-IR and CD measurements. Preliminary molecular mechanics calculations were also performed on some synthetic peptides. Pharmacological screening using the relaxation of the isolated rat duodenum preparation showed that incorporation of N -benzylglycine at positions 5 and/or 8 in the linear Thr6 -BK causes a substantial decrease in potency. Comparable incorporation in cyclo Thr6 -BK, at position 8, or 5 and 8, resulted in nearly inactive analogues. However, cyclo BzlGly5,Thr6 -BK showed a potency which is of the same order of magnitude as for cyclo -BK and cyclo Thr6 -BK. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] A new amino acid derivative with a masked side-chain aldehyde and its use in peptide synthesis and chemoselective ligationJOURNAL OF PEPTIDE SCIENCE, Issue 10 2001Jane C. Spetzler Abstract A new amino acid derivative with a diol side-chain, ,,-2-amino-4,5-dihydroxy-pentanoic acid (Adi), has been prepared from ,,-allylglycine by suitable protection, for use in peptide synthesis, as Fmoc-,,-Adi(Trt)2. This building block enables the introduction of a side-chain aldehyde at any position in a given peptide sequence without use of specialized side-chain protection schemes. The aldehyde is revealed by mild oxidation with sodium periodate, circumventing the problematic release of reactive peptidic aldehydes in TFA solution. Peptides with aldehyde side-chains are useful for chemo-selective ligation, reacting selectively with oxyamines to yield oxime links, while all other peptide functions can be left unprotected. The utility of the new building block has been demonstrated by the synthesis of peptide dimers and a cyclo-peptide. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] Use of peptide for selective and sensitive detection of an Anthrax biomarker via peptide recognition and surface-enhanced Raman scatteringJOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2010Kyungtag Ryu Abstract A short 16-amino acid peptide has been used in place of an antibody to selectively detect the specific Anthrax biomarker, protective antigen (PA), using surface-enhanced Raman scattering (SERS). Peptides are more stable than antibodies under various biological conditions and are easily synthesized for a specific target. A peptide that has high affinity to PA was conjugated onto gold nanoparticles along with a Raman reporter and then incubated in various concentrations of PA. Parallel studies in which the peptide sequence was replaced with an antibody were performed to compare the performance of the two methodologies. Both the peptide and antibody functionalized nanoparticles were able to specifically detect PA concentrations down to 6.1 fM. These results demonstrate that these short, robust peptides can be used in the place of traditional antibodies to specifically recognize target biomarkers in the field for the potential diagnosis of disease. Copyright © 2010 John Wiley & Sons, Ltd. [source] Protein glycosylation analysis by HILIC-LC-MS of Proteinase K-generated N - and O -glycopeptidesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 6-7 2010Gerhild Zauner Abstract Analysis of protein glycosylation is essential in order to correlate certain disease types with oligosaccharide structures on proteins. Here, a method for the MS characterization of site-specific protein glycosylation is presented. Using asialofetuin and fetuin as model substances, a protocol for glycopeptide dissection was developed based on unspecific proteolysis by Proteinase K. The resulting glycopeptides were then resolved by nanoscale hydrophilic interaction liquid chromatography-electrospray multistage MS. The early elution range of O -glycopeptides was clearly separated from the late elution range of N -glycopeptides. Glycopeptides were analyzed by ion trap-MS/MS, which revealed fragmentations of glycosidic linkages and some peptide backbone cleavages; MS3 spectra predominantly exhibited cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N - and O -glycan attachment sites of fetuin could be confirmed; moreover using our method, the occupation of a new, additional O -glycosylation site serine 296 was found. In conclusion, this approach appears to be a valuable technique for in-depth analysis of the site-specific N -glycosylation and O -glycosylation of individual glycoproteins. [source] Oral vaccination with envelope protein VP28 against white spot syndrome virus in Procambarus clarkii using Bacillus subtilis as delivery vehiclesLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2008L.L. Fu Abstract Aims:, To achieve high-level expression and secretion of active VP28 directed by a processing-efficient signal peptide in Bacillus subtilis WB600 and exploit the possibility of obtaining an oral vaccine against white spot syndrome virus (WSSV) using vegetative cells or spores as delivery vehicles. Methods and Results:, The polymerase chain reaction (PCR)-amplified vp28 gene was inserted into a shuttle expression vector with a novel signal peptide sequence. After electro-transformation, time-courses for recombinant VP28 (rVP28) secretion level in B. subtilis WB600 were analysed. Crayfish were divided into three groups subsequently challenged by 7-h immersion at different time points after vaccination. Subgroups including 20 inter-moult crayfish with an average weight of 15 g in triplicate were vaccinated by feeding coated food pellets with vegetative cells or spores for 20 days. Vaccination trials showed that rVP28 by spore delivery induced a higher resistance than using vegetative cells. Challenged at 14 days postvaccination, the relative per cent survival (RPS) values of groups of rVP28-bv and rVP28-bs was 51·7% and 78·3%, respectively. Conclusions:, The recombinant B. subtilis strain with the ability of high-level secretion of rVP28 can evoke protection of crayfish against WSSV by oral delivery. Significance and Impact of the Study:, Oral vaccination by the B. subtilis vehicle containing VP28 opens a new way for designing practical vaccines to control WSSV. [source] Bioengineered ,golden' indica rice cultivars with ,-carotene metabolism in the endosperm with hygromycin and mannose selection systemsPLANT BIOTECHNOLOGY JOURNAL, Issue 2 2003Karabi Datta Summary Vitamin-A deficiency (VAD) is a major malnutrition problem in South Asia, where indica rice is the staple food. Indica-type rice varieties feed more than 2 billion people. Hence, we introduced a combination of transgenes using the biolistic system of transformation enabling biosynthesis of provitamin A in the endosperm of several indica rice cultivars adapted to diverse ecosystems of different countries. The rice seed-specific glutelin promoter (Gt-1 P) was used to drive the expression of phytoene synthase (psy), while lycopene ,-cyclase (lcy) and phytoene desaturase (crtI), fused to the transit peptide sequence of the pea-Rubisco small subunit, were driven by the constitutive cauliflower mosaic virus promoter (CaMV35S P). Transgenic plants were recovered through selection with either CaMV35S P driven hph (hygromycin phosphotransferase) gene or cestrum yellow leaf curling virus promoter (CMP) driven pmi (phophomannose isomerase) gene. Molecular and biochemical analyses demonstrated stable integration and expression of the transgenes. The yellow colour of the polished rice grain evidenced the carotenoid accumulation in the endosperm. The colour intensity correlated with the estimated carotenoid content by spectrophotometric and HPLC analysis. Carotenoid level in cooked polished seeds was comparable (with minor loss of xanthophylls) to that in non-cooked seeds of the same transgenic line. The variable segregation pattern in T1 selfing generation indicated single to multiple loci insertion of the transgenes in the genome. This is the first report of using nonantibiotic pmi driven by a novel promoter in generating transgenic indica rice for possible future use in human nutrition. [source] Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 19 2010Tatiana Yu Perlova Abstract LC combined with MS/MS analysis of complex mixtures of protein digests is a reliable and sensitive method for characterization of protein phosphorylation. Peptide retention times (RTs) measured during an LC-MS/MS run depend on both the peptide sequence and the location of modified amino acids. These RTs can be predicted using the LC of biomacromolecules at critical conditions model (BioLCCC). Comparing the observed RTs to those obtained from the BioLCCC model can provide additional validation of MS/MS-based peptide identifications to reduce the false discovery rate and to improve the reliability of phosphoproteome profiling. In this study, energies of interaction between phosphorylated residues and the surface of RP separation media for both "classic" alkyl C18 and polar-embedded C18 stationary phases were experimentally determined and included in the BioLCCC model extended for phosphopeptide analysis. The RTs for phosphorylated peptides and their nonphosphorylated analogs were predicted using the extended BioLCCC model and compared with their experimental RTs. The extended model was evaluated using literary data and a complex phosphoproteome data set distributed through the Association of Biomolecular Resource Facilities Proteome Informatics Research Group 2010 study. The reported results demonstrate the capability of the extended BioLCCC model to predict RTs which may lead to improved sensitivity and reliability of LC-MS/MS-based phosphoproteome profiling. [source] Predictions of peptides' retention times in reversed-phase liquid chromatography as a new supportive tool to improve protein identification in proteomicsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2009Tomasz B, czek Dr. Abstract One of the initial steps of proteomic analysis is peptide separation. However, little information from RP-HPLC, employed for peptides separation, is utilized in proteomics. Meanwhile, prediction of the retention time for a given peptide, combined with routine MS/MS data analysis, could help to improve the confidence of peptide identifications. Recently, a number of models has been proposed to characterize quantitatively the structure of a peptide and to predict its gradient RP-HPLC retention at given separation conditions. The chromatographic behavior of peptides has usually been related to their amino acid composition. However, different values of retention coefficients of the same amino acid in different peptides at different neighborhoods were commonly observed. Therefore, specific retention coefficients were derived by regression analysis or by artificial neural networks (ANNs) with the use of a set of peptides retention. In the review, various approaches for peptide elution time prediction in RP-HPLC are presented and critically discussed. The contribution of sequence dependent parameters (e.g., amphipathicity or peptide sequence) and peptide physicochemical descriptors (e.g., hydrophobicity or peptide length) that have been shown to affect the peptide retention time in LC are considered and analyzed. The predictive capability of the retention time prediction models based on quantitative structure,retention relationships (QSRRs) are discussed in details. Advantages and limitations of various retention prediction strategies are identified. It is concluded that proper processing of chromatographic data by statistical learning techniques can result in information of direct use for proteomics, which is otherwise wasted. [source] | ||||||||||||||||||||||||||||||||||||||||