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Peptide Fragments (peptide + fragment)
Selected AbstractsConformational Preferences of Short Peptide Fragments,ANGEWANDTE CHEMIE, Issue 46 2009Yoshiyuki Hatakeyama Faltung auf engstem Raum: Tri- bis Hexapeptide wurden durch eine synthetische Wirtstruktur in Wasser eingeschlossen und falteten sich dabei in ihre latenten helicalen Strukturen (siehe Bild). Kristallographische Analysen der Komplexe belegen eine gemischte Konformation mit 310 - und ,-Helices und somit die Neigung kurzer Peptidfragmente zum Aufbau von Helices. [source] A fast, reproducible and low-cost method for sequence deconvolution of ,on-bead' peptides via ,on-target' maldi-TOF/TOF mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2010Giulio A. Amadei Abstract A novel approach to high-throughput sequence deconvolution of on-bead small peptides (MW < 2000 Da) using on-target MALDI-TOF/TOF instrumentation is presented. Short peptides of pentamer and octamer length, covalently attached to TentaGel polystyrene beads through a photolabile linker, were placed onto the MALDI target, apportioned with suitable matrix (2,5-dihydroxybenzoic acid) and then hit with the instrument laser (Nd : YAG, 355 nm). This induced easy and highly reproducible photochemical cleavage, desorption (MS mode) and fragmentation (MS/MS mode). Peptide fragments were identified with a mass accuracy of 0.1 Da of the expected values. This technique significantly accelerates the sequence determination of positive peptide hits obtained from random combinatorial libraries when screening against biological targets, paving the way for a rapid and efficient method to identify molecular imaging ligands specific to pathological targets in cancer and other diseases. Copyright © 2009 John Wiley & Sons, Ltd. [source] Capillary liquid chromatography/atmospheric-pressure matrix-assisted laser desorption/ionisation ion trap mass spectrometry: a comparison with liquid chromatography/matrix-assisted laser desorption/ionisation time-of-flight and liquid chromatography/electrospray ionisation quadrupole time-of-flight for the identification of tryptic peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2006Colin S. Creaser The atmospheric-pressure matrix-assisted laser desorption/ionisation quadrupole ion trap (AP-MALDI-QIT) analysis of tryptic peptides is reported following capillary liquid chromatographic (LC) separation and direct analysis of a protein digest. Peptide fragments were identified by peptide mass fingerprinting from mass spectrometric data and sequence analysis obtained by tandem mass spectrometry of the principal mass spectral peaks using a data-dependent scanning protocol. These data were compared with those from mass spectrometric analysis using capillary LC/MALDI-time-of-flight (TOF) and capillary LC/electrospray ionisation (ESI)-quadrupole TOF. For all three configurations the resulting data were searched against the MSDB database, using MASCOT and the sequence coverage compared for each technique. Complementary data were obtained using the three techniques. Copyright © 2006 John Wiley & Sons, Ltd. [source] Peptide-doxorubicin conjugates specifically degraded by matrix metalloproteinases expressed from tumorDRUG DEVELOPMENT RESEARCH, Issue 5 2006Gee Young Lee Abstract Specific peptide-doxorubicin conjugates were developed for targeting matrix metalloproteinases (MMPs) expressed from tumors. The peptide-doxorubicin conjugates were designed to be cleaved by MMP-2 and MMP-9 in order that doxorubicin or the active form that acts as an anticancer agent was released free from the peptide fragment at the tumor site. Three types of peptide-doxorubicin conjugates were synthesized using the peptides: GPLG (Gly-Pro-Leu-Gly), GPLGV (Gly-Pro-Leu-Gly-Val), and GPLGPAG (Gly-Pro-Leu-Gly-Pro-Ala-Gly). The synthesized peptide-doxorubicin conjugates were characterized for their degradation behavior and bioactivity in vitro, and their antitumoral activity was assessed using the Lewis lung carcinoma (LLC) model, which expresses MMP-2 and MMP-9. After incubation with active MMP-2 for 24,h, GPLG-doxorubicin was barely degraded, whereas GPLGV-doxorubicin and GPLGPAG-doxorubicin were considerably degraded by active MMP-2. Consequently, all peptide-doxorubicin conjugates had significantly low cytotoxicity compared to doxorubicin, but tumor growth suppression was exhibited only by GPLGV-doxorubicin and GPLGPAG-doxorubicin. The tumor growth suppression by the two conjugates was higher compared to control, although it did not exceed the suppression level shown by doxorubicin. The low toxicity exhibited by peptide-doxorubicin conjugates resulted in only slight body weight loss in mice, whereas doxorubicin greatly reduced body weight and induced severe side effects. Therefore, we propose MMPs-specific peptide-doxorubicin conjugates in targeting anti-cancer drug delivery that could reduce systemic toxicities. Drug Dev. Res. 67:438,447, 2006. © 2006 Wiley-Liss, Inc. [source] Biophysical studies of the development of amyloid fibrils from a peptide fragment of cold shock protein BFEBS JOURNAL, Issue 9 2000Deborah K. Wilkins The peptide CspB-1, which represents residues 1,22 of the cold shock protein CspB from Bacillus subtilis, has been shown to form amyloid fibrils when solutions containing this peptide in aqueous (50%) acetonitrile are diluted in water [M. Großet al. (1999) Protein Science8, 1350,1357] We established conditions in which reproducible kinetic steps associated with the formation of these fibrils can be observed. Studies combining these conditions with a range of biophysical methods reveal that a variety of distinct events occurs during the process that results in amyloid fibrils. A CD spectrum indicative of ,,structure is observed within 1 min of the solvent shift, and its intensity increases on a longer timescale in at least two kinetic phases. The characteristic wavelength shift of the amyloid-binding dye Congo Red is established within 30 min of the initiation of the aggregation process and corresponds to one of the phases observed by CD and to changes in the Fourier transform-infrared spectrum indicative of ,,structure. Short fibrillar structures begin to be visible under the electron microscope after these events, and longer, well-defined amyloid fibrils are established on a timescale of hours. NMR spectroscopy shows that there are no significant changes in the concentration of monomeric species in solution during the events leading to fibril formation, but that soluble aggregates too large to be visible in NMR spectra are present throughout the process. A model for amyloid formation by this peptide is presented which is consistent with these kinetic data and with published work on a variety of disease-related systems. These findings support the concept that the ability to form amyloid fibrils is a generic property of polypeptide chains, and that the mechanism of their formation is similar for different peptides and proteins. [source] Solid-phase synthesis of cyclic analogues related to the hypoglycaemic peptide hGH[6,13]: Comparison of two i,i+4 lactam cyclization proceduresJOURNAL OF PEPTIDE SCIENCE, Issue 10 2001Vittoria Cavallaro Abstract The use of 1,3-diisopropylcarbodiimide (DIC) for the synthesis of cyclic analogues of the hypoglycaemic peptide fragment derived from the N -terminus of human growth hormone (hGH), namely hGH[6,13], is described. Different strategies were examined to achieve improved yields for the on resin side-chain to side-chain cyclization of the corresponding linear peptides containing reverse , - turn motifs. When compared with the more reactive Castro's reagent, the results confirm that DIC in the presence of HOBt can be successfully employed to minimize the formation of intermolecular oligomeric by-products associated with the preparation of cyclic hGH[6,14] peptide analogues based on an i,(i+4)Lys,Glu or Glu,Lys cyclization strategy. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] Pharmaceutical and immunological evaluation of human papillomavirus viruslike particle as an antigen carrierJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 1 2006Roxana M. Ionescu Abstract We report the preparation and the immunogenicity of a conjugate vaccine obtained by chemically conjugating a variant of the extracellular peptide fragment of influenza type A M2 protein to the human papillomavirus (HPV) viruslike particle (VLP). Conjugates comprised of approximately 4000 copies of the antigenic peptide per VLP are obtained as the result of the reaction between a C-terminal cysteine residue on the peptide and the maleimide-activated HPV VLP. The resulting conjugates have an average particle size slightly larger than the carrier and present enhanced overall stability against chemical and thermal-induced denaturation. The M2-HPV VLP conjugates lost the binding affinity for anti-HPV conformational antibodies but retained reactivity to a M2-specific monoclonal antibody. The conjugate vaccine formulated with aluminum adjuvant and delivered in two doses of 30-ng peptide was found to be highly immunogenic and conferred good protection against lethal challenge of influenza virus in mice. These results suggest that HPV VLP can be used as a carrier for synthetic or small antigens for the development of subunit vaccines. © 2005 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 95:70,79, 2006 [source] NPP1, a Phytophthora -associated trigger of plant defense in parsley and ArabidopsisTHE PLANT JOURNAL, Issue 3 2002Guido Fellbrich Summary Activation of non-cultivar-specific plant defense against attempted microbial infection is mediated through the recognition of pathogen-derived elicitors. Previously, we have identified a peptide fragment (Pep-13) within a 42-kDa cell wall transglutaminase from various Phytophthora species that triggers a multifacetted defense response in parsley cells. Many of these oomycete species have now been shown to possess another cell wall protein (24 kDa), that evoked the same pattern of responses in parsley as Pep-13. Unlike Pep-13, necrosis-inducing Phytophthora protein 1 (NPP1) purified from P. parasitica also induced hypersensitive cell death-like lesions in parsley. NPP1 structural homologs were found in oomycetes, fungi, and bacteria, but not in plants. Structure,activity relationship studies revealed the intact protein as well as two cysteine residues to be essential for elicitor activity. NPP1-mediated activation of pathogen defense in parsley does not employ the Pep-13 receptor. However, early induced cellular responses implicated in elicitor signal transmission (increased levels of cytoplasmic calcium, production of reactive oxygen species, MAP kinase activation) were stimulated by either elicitor, suggesting the existence of converging signaling pathways in parsley. Infiltration of NPP1 into leaves of Arabidopsis thaliana Col-0 plants resulted in transcript accumulation of pathogenesis-related (PR) genes, production of ROS and ethylene, callose apposition, and HR-like cell death. NPP1-mediated induction of the PR1 gene is salicylic acid-dependent, and, unlike the P. syringae pv. tomato DC3000(avrRpm1)-induced PR1 gene expression, requires both functional NDR1 and PAD4. In summary, Arabidopsis plants infiltrated with NPP1 constitute an experimental system that is amenable to forward genetic approaches aiming at the dissection of signaling pathways implicated in the activation of non-cultivar-specific plant defense. [source] Factors affecting proliferation and differentiation of lepidopteran midgut stem cells,ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 1 2010Marcia J. Loeb Midgut stem cells of last instar larvae and pupae of Heliothis virescens, Lymantria dispar and several other Lepidopteran species have been cultured in vitro and have been induced to proliferate using low titers of ecdysteroids and the 77-Kda peptide fragment, ,-arylphorin, isolated and identified from pupal fat body tissue. The insulin-related hormone, Bombyxin, also induced mitosis in cultured midgut stem cells; it appeared to be fast-acting and quickly inactivated, while ,-arylphorin was slower to act and had a longer lasting effect in vitro, indicating different functions for these proliferation agents. Changes in Calcium ion concentration within or outside the cells discretely affected stem cell differentiation, indicating a role for second messenger participation in peptide regulation of this process. Four different peptides (MDFs 1,4) that induced midgut stem cells to differentiate to mature midgut cell types in vitro were isolated and characterized from conditioned media and hemolymph of H. virescens and L. dispar. However, platelet-derived growth factor (PDGF), epidermal growth factor (EGF), and all-trans retinoic acid (RA) from vertebrate sources induced differentiation to non-midgut cell types as well. MDF1 was located in basal areas of columnar cells of midgut epithelium, although MDF2 was observed in all of the cytoplasm of columnar cells and in droplets of antibody positive material in the midgut lumen, suggesting a digestive function as well for this peptide. Anti-MDF-3 stained the central areas of cultured midgut columnar cells and the bases of columnar cells of midgut epithelium in vivo. Midgut secretory cells stained with anti-MDF-4; streams of MFD-4-positive material were observed extending from secretory cells facing the epithelial lumen, and as a layer on the hemolymph-facing side, suggesting an endocrine or paracrine function for this or an immunologically similar peptide. Published 2010 Wiley Periodicals, Inc. [source] Structure of the Fab fragment from F124, a monoclonal antibody specific for hepatitis B surface antigenACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2000F. A. Saul The crystal structure of the Fab fragment from the monoclonal anti-preS2 antibody F124 (IgG1,,) has been solved by molecular replacement and refined at 3.0,Å resolution. The Fab crystallizes with two independent molecules in the asymmetric unit. F124 recognizes an epitope contained within the preS2 segment between residues 120 and 132 of the surface antigen of hepatitis B virus. The antibody shows a high affinity for the glycan N-linked to Asn123, but it also cross-reacts with the non-glycosylated peptide fragment 120,132. Although crystallization was performed in the presence of an eightfold excess of the cross-reactive peptide, no evidence for the ligand was found in the antigen-binding site, which is close to a neighbouring molecule in the crystal lattice. The antigen-binding site has a groove-like topology which is modulated with pocket-like cavities. It is characterized by a large number of tyrosine and aspartate residues. The importance of germ-line mutations at the binding site is discussed. [source] Methotrexate for psoriasis in the era of biological therapyCLINICAL & EXPERIMENTAL DERMATOLOGY, Issue 5 2008R. B. Warren Summary Methotrexate's traditional role as a first line agent for moderate to severe psoriasis is being challenged by the rapid and growing use of biological therapies. A recent study comparing adalimumab with methotrexate showed significantly superior efficacy of adalimumab over methotrexate over 16 weeks. Although it is inexpensive, the future use of methotrexate may be compromised by its unpredictable response and toxicity, and by the introduction of newer, more effective biological therapies. However, recent advances in the screening of liver fibrosis by monitoring serum levels of the aminoterminal peptide fragment of type III procollagen have reduced the need for liver biopsy. Furthermore, the potential for personalized methotrexate use by application of modern pharmacogenetics and pharmacokinetics may ensure its place as a first-line agent for the treatment of psoriasis for the foreseeable future. [source] A novel 2D-based approach to the discovery of candidate substrates for the metalloendopeptidase meprinFEBS JOURNAL, Issue 18 2008Daniel Ambort In the past, protease-substrate finding proved to be rather haphazard and was executed by in vitro cleavage assays using singly selected targets. In the present study, we report the first protease proteomic approach applied to meprin, an astacin-like metalloendopeptidase, to determine physiological substrates in a cell-based system of Madin,Darby canine kidney epithelial cells. A simple 2D IEF/SDS/PAGE-based image analysis procedure was designed to find candidate substrates in conditioned media of Madin,Darby canine kidney cells expressing meprin in zymogen or in active form. The method enabled the discovery of hitherto unkown meprin substrates with shortened (non-trypsin-generated) N- and C-terminally truncated cleavage products in peptide fragments upon LC-MS/MS analysis. Of 22 (17 nonredundant) candidate substrates identified, the proteolytic processing of vinculin, lysyl oxidase, collagen type V and annexin A1 was analysed by means of immunoblotting validation experiments. The classification of substrates into functional groups may propose new functions for meprins in the regulation of cell homeostasis and the extracellular environment, and in innate immunity, respectively. [source] Identification of domains on the extrinsic 23 kDa protein possibly involved in electrostatic interaction with the extrinsic 33 kDa protein in spinach photosystem IIFEBS JOURNAL, Issue 5 2004Akihiko Tohri To elucidate the domains on the extrinsic 23 kDa protein involved in electrostatic interaction with the extrinsic 33 kDa protein in spinach photosystem II, we modified amino or carboxyl groups of the 23 kDa protein to uncharged methyl ester groups with N -succinimidyl propionate or glycine methyl ester in the presence of a water-soluble carbodiimide, respectively. The N -succinimidyl propionate-modified 23 kDa protein did not bind to the 33 kDa protein associated with PSII membranes, whereas the glycine methyl ester-modified 23 kDa protein completely bound. This indicates that positive charges on the 23 kDa protein are important for electrostatic interaction with the 33 kDa protein associated with the PSII membranes. Mapping of the N -succinimidyl propionate-modified sites of the 23 kDa protein was performed using Staphylococcus V8 protease digestion of the modified protein followed by determination of the mass of the resultant peptide fragments with MALDI-TOF MS. The results showed that six domains (Lys11,Lys14, Lys27,Lys38, Lys40, Lys90,Lys96, Lys143,Lys152, Lys166,Lys174) were modified with N -succinimidyl propionate. In these domains, Lys11, Lys13, Lys33, Lys38, Lys143, Lys166, Lys170 and Lys174 were wholly conserved in the 23 kDa protein from 12 species of higher plants. These positively charged lysyl residues on the 23 kDa protein may be involved in electrostatic interactions with the negatively charged carboxyl groups on the 33 kDa protein, the latter has been suggested to be important for the 23 kDa binding [Bricker, T.M. & Frankel, L.K. (2003) Biochemistry42, 2056,2061]. [source] Monoclonal and polyclonal humoral immune response to EC HER-2/NEU peptides with low similarity to the host's proteomeINTERNATIONAL JOURNAL OF CANCER, Issue 5 2002Abraham Mittelman Abstract We are studying peptide immunogenicity as a function of the similarity level to the host's proteome. By using as a model the breast/prostate cancer-associated HER-2/neu antigen, we analyzed the monoclonal and polyclonal humoral immune responses against HER-2/neu peptide motifs not shared with the host proteome. We show here that (i) a mouse monoclonal antibody (MAb) raised against the extracellular domain (EC) of human HER-2/neu oncoprotein recognized a linear peptide motif endowed with low similarity level to the mouse proteome; (ii) likewise, human sera from breast/prostate cancer patients preferentially recognized peptide fragments from the EC of the HER-2/neu oncoprotein having sequences that are not present in the human proteome. Together with previous results obtained in other disease models (cervical cancer-associated HPV16 E7 oncoprotein and Pemphigus vulgaris auto-antigen desmoglein-3), the present data suggest that a low level of sequence similarity to the host's proteome might be an important factor in shaping the pool of B cell epitopes. © 2002 Wiley-Liss, Inc. [source] A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: Mixed basis set and ONIOM methods combined with a complete basis set extrapolationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2006Seongho Moon Abstract This article compares several quantum mechanical approaches to the computation of chemical shielding tensors in peptide fragments. First, we describe the effects of basis set quality up to the complete basis set (CBS) limit and level of theory (HF, MP2, and DFT) for four different atoms in trans N -methylacetamide. For both isotropic shielding and shielding anisotropy, the MP2 results in the CBS limit show the best agreement with experiment. The HF values show quite a different tendency to MP2, and even in the CBS limit they are far from experiment for not only the isotropic shielding of carbonyl carbon but also most shielding anisotropies. In most cases, the DFT values differ systematically from MP2, and small basis-set (double- or triple-zeta) results are often fortuitously in better agreement with the experiment than the CBS ones. Second, we compare the mixed basis set and ONIOM methods, combined with CBS extrapolation, for chemical shielding calculations at a DFT level using various model peptides. From the results, it is shown that the mixed basis set method provides better results than ONIOM, compared to CBS calculations using the nonpartitioned full systems. The information studied here will be useful in guiding the selection of proper quantum chemical models, which are in a tradeoff between accuracy and cost, for shielding studies of peptides and proteins. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 825,836, 2006 [source] Lattice models of peptide aggregation: Evaluation of conformational search algorithmsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2005Mark T. Oakley Abstract We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa,Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1638,1646, 2005 [source] WHEN POSITIVELY CHARGED MILK PROTEINS CAN BIND TO DNAJOURNAL OF FOOD BIOCHEMISTRY, Issue 6 2002MAHMOUD SITOHY ABSTRACT The binding of three esterified milk proteins (,-lactoglobutin, ,-lactalbumin and ,-casein) to plasmid DNAs at pH 7.1 was followed by agarose-gel electrophoresis. Highly esterified ,-lactoglobulin and ,-lactalbumin samples showed DNA-binding capacities comparable to those exhibited by native basic proteins such as lysozymes and histones. All the studied esterified ,-casein samples failed to bind to DNA at the applied pH. Complete retardation of DNA migration on agarose gel was observed at a 1:1 ratio of protein basic groups (Lys + Arg) to DNA phosphate add groups in the case of highly esterified ,-lactoglobulin, esterified ,-lactalbumin and native basic proteins (lysozyme and histone). Binding capacity was dependent on the degree of esterification of the milk proteins. Hydrolysis of esterified milk proteins either suppressed or reduced their DNA-binding capacities according to the degree of hydrolysis and consequently to the average size of the resulting peptides. A prolonged peptic hydrolysis (25% degree of hydrolysis) completely suppressed DNA-binding capacity probably because of the small sizes of the resulting peptic peptides (< 1 kDa). Treatment with trypsin, which hydrolyzed the esterified proteins into relatively large peptide fragments, reduced the DNA-binding capacity to levels inversely proportional to the degree of hydrolysis. In the range of 2.7,12.3 kb, there was no influence of the DNA size on the binding of esterified milk proteins. The interactions DNA-esterified milk proteins did not depend on the DNA shape (circular or linear). Circular dichroism spectra of DNA in complex with methylated ,-lactoglobulin were markedly altered as compared to those obtained when DNA was in complex with native ,-lactoghbutin. [source] Systematic epitope analysis of the p26 EIAV core proteinJOURNAL OF MOLECULAR RECOGNITION, Issue 4 2007Adriana Soutullo Abstract The major core protein of equine infectious anemia virus (EIAV), p26, is one of the primary immunogenic structural proteins during a persistent infection of horses and is highly conserved among antigenically variants of viral isolates. In order to investigate its immune profile in more detail for a better diagnostic, an epitope mapping was carried out by means of two libraries of overlapping peptide fragments prepared by simultaneous and parallel SPPS on derivatized cellulose membranes (SPOT synthesis). Polyclonal equine sera from infected horses were used for the biological assay. Particularly two promising continuous epitopes (NAMRHL and MYACRD) were localized on the C-terminal extreme of p26, region 194,222. A cyclic synthetic fragment of 29 amino acid residues containing the identified epitopes was designed and studied. A significant conformational change towards a helical structure was observed when the peptide was cyclized by a bridge between Cys198 and Cys218. This observation correlated with an improvement of its ability to be recognized by specific antibodies in an EIA (Enzyme-linked Immunosorbent assay). These results suggest that the conformationally restricted synthetic antigen adequately mimics the native structure of this region of p26 core protein. Copyright © 2007 John Wiley & Sons, Ltd. [source] Biosynthesis of peptide fragments of eukaryotic GPCRs in Escherichia coli by directing expression into inclusion bodiesJOURNAL OF PEPTIDE SCIENCE, Issue 5 2010Leah S. Cohen Abstract Biosynthesis of peptides in heterologous systems is often a prerequisite to biophysical analyses. Large amounts of peptides, in particular portions of membrane proteins, are needed to optimize conditions for secondary and tertiary structure analysis. Chemical synthesis of these peptides is limited by their high hydrophobicity and also due to the need to incorporate isotopic labels for high resolution NMR analysis. In this protocol, we describe a method for the heterologous expression and purification of unlabeled and isotopically labeled peptide fragments of Ste2p, an integral membrane G protein-coupled receptor. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source] Identification of three novel peptides isolated from the venom of the neotropical social wasp Polistes major majorJOURNAL OF PEPTIDE SCIENCE, Issue 7 2007Václav, ovský Abstract Three novel peptides designated as PMM1, PMM2, and PMM3 were isolated and characterized from the venom of the social wasp Polistes major major, one of the most common wasps in the Dominican Republic. By Edman degradation, and MALDI-TOF and ESI-QTOF mass spectrometry, the primary sequences of these peptides were established as follows: PMM1, H-Lys-Arg-Arg-Pro-Pro-Gly-Phe-Thr-Pro-Phe-Arg-OH (1357.77 Da); PMM2, H-Ile-Asn-Trp-Lys-Lys-Ile-Ala-Ser-Ile-Gly-Lys-Glu-Val-Leu-Lys-Ala-Leu-NH2 (1909.19 Da); and PMM3, H-Phe-Leu-Ser-Ala-Leu-Leu-Gly-Met-Leu-Lys-Asn-Leu-NH2 (1317.78 Da). The suggested sequences were confirmed by MS analysis of peptide fragments obtained by enzymatic digestion. The peptide PMM1 is a lysyl-arginyl-Thr6 -bradykinine that belongs to the wasp kinins group. The sequence of the PMM2 peptide is unique; it resembles somewhat the tetradecapeptide amides of the mastoparan group; however, the chain is extended by three additional amino acid residues. The sequence of PMM3 dodecapeptide is homologous to the peptides of the wasp chemotactic group. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] An enigmatic peptide ligation reaction: Protease-catalyzed oligomerization of a native protein segment in neat aqueous solutionPROTEIN SCIENCE, Issue 4 2000Sangaralingam Kumaran Abstract We report an enigmatic peptide ligation reaction catalyzed by Glu-specific Staphylococcus aureus V8 protease that occurs in neat aqueous solution around neutral pH utilizing a totally unprotected peptide substrate containing free ,-carboxyl and ,-amino groups. V8 protease catalyzed a chain of ligation steps between pH 6 and 8 at 4 °C, producing a gamut of covalent oligomers (dimer through octamer or higher) of a native protein segment TAAAKFE (S39) derived from ribonuclease A (RNAse A). Size-exclusion chromatography suggested the absence of strong interaction between the reacting peptides. The circular dichroism spectra of monomer through pentamer showed length-dependent enhancement of secondary structure in the oligomers, suggesting that protease-catalyzed ligation of a monomer to an oligomer resulted in a product that was more structured than its precursor. The relative conformational stability of the oligomers was reflected in their ability to resist proteolysis, indicating that the oligomerization reaction was facilitated as a consequence of the "conformational trapping" of the product. The ligation reaction proceeded in two phases,slow formation and accumulation of the dimer followed by a fast phase of oligomerization, implying that the conformational trap encountered in the oligomerization reaction was a two-step process. The Gly substitution at any position of the TAAAKFE sequence was deleterious, suggesting that the first step of the conformational trap, namely the dimerization reaction, that proceeded very slowly even with the parent peptide, was quite sensitive to amino acid sequence. In contrast, the oligomerization reaction of an Ala analog, AAAAKFE, occurred in much the same way as S39, albeit with faster rate, suggesting that Ala substitution stabilized the overall conformational trapping process. The results suggest the viability of the product-directed "conformational trap" as a mechanism to achieve peptide ligation of totally unprotected peptide fragments in neat aqueous solution. Further, the study projects the presence of considerable innate synthetic potential in V8 protease, baring rich possibilities of protein engineering of this enzyme to generate a "V8 peptide ligase." [source] High-resolution imaging and proteomics of peptide fragments by TOF-SIMSPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2010Håkan Nygren Abstract Thyroglobulin is an iodinated glycoprotein (m.w. 660,kD) required for the storage and formation of thyroid hormone. Thyroglobulin was digested by trypsin in distilled water and the resulting peptides were identified by TOF-secondary ion mass spectrometry, using TFA as a matrix to catalyze the ionization of the peptides. Cryostate sections of pig thyroid glands were incubated with trypsin in distilled water, followed by deposition of TFA. The sections were analyzed with TOF-secondary ion mass spectrometry, and the peptides formed were identified through comparison with the peptides of the thyroglobulin reference sample. The thyroglobulin fragments were localized in the thyroid follicle cells with a spatial resolution of 3 microns, a mass resolution m/,m of >6000 and a mass accuracy of <60,ppm. The thyroglobulin was found localized heterogeneously in the follicle cells. The heterogeneity may be due to thyroglobulin synthesis, uptake and degradation or globules representing insoluble polymers of thyroglobulin considered to be a mechanism for storing hormone at high concentrations. [source] Investigating the structural properties of amyloid-like fibrils formed in vitro from ,2 -microglobulin using limited proteolysis and electrospray ionisation mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 11 2006Sarah L. Myers The protein ,2 -microglobulin (,2m) aggregates to form classical amyloid fibrils in patients undergoing long-term haemodialysis. Amyloid-like fibrils with a cross- , fold can also be formed from wild-type ,2m under acidic conditions in vitro. The morphology of such fibrils depends critically on the conditions used: incubation of ,2m in low ionic strength buffers at pH 2.5 results in the formation of long (µm), straight fibrils while, at pH 3.6, short (<500,nm) fibrils form. At higher ionic strengths (0.2,0.4,M) at pH 1.5,3.6, the fibrils have a distinct curved and nodular morphology. To determine the conformational properties of ,2m within in vitro fibrils of different morphologies, limited proteolysis of each fibril type using pepsin was performed and the resulting peptide fragments identified by tandem mass spectrometry. For comparison, the proteolytic degradation patterns of monomeric ,2m and seven synthetic peptides spanning the entire sequence of the intact protein were similarly analysed. The results show that fibrils with different morphologies result in distinct digestion patterns. While the curved, worm-like fibrils are relatively weakly protected from proteolysis, the long, straight fibrils formed at pH 2.5 at low ionic strength show only a single cut-site at Val9, demonstrating that substantial refolding of the initially acid-denatured and unprotected state of ,2m occurs during assembly. The data demonstrate that the organisation of the polypeptide chain in fibrils with different morphological features differs considerably, despite the fact that the fibrils possess a common cross- , architecture. Copyright © 2006 John Wiley & Sons, Ltd. [source] DNA microarray analyses of the effects of dietary proteinsBIOFACTORS, Issue 1-4 2004Hisanori Kato Abstract Dietary proteins and amino acids serve not only as a building block for body components but also as regulators of a variety of body functions. A great many of the functions of ingested proteins, their peptide fragments, and amino acids have been characterized and some have been brought to practical application. Using a GeneChip DNA microarray system, we first compared the gene expression profiles among rats fed on 12% casein, 12% gluten, and protein-free diets for one week. The results revealed that a few hundred genes in the liver and muscle were up- or down-regulated by more than two-fold after feeding of the gluten or the protein-free diet. Interesting findings included the induction of genes for synthesis and catabolism of cholesterol by gluten feeding. In addition, we performed a study to examine the effect of the consumption of an enzymatically produced, hypoallergenic wheat flour on gene expression profiles in rats. The results confirmed the safety of this novel food product. [source] Analysis of oxidation process of cholecystokinin octapeptide with reactive oxygen species by high-performance liquid chromatography and subsequent electrospray ionization mass spectrometryBIOMEDICAL CHROMATOGRAPHY, Issue 2 2010Hideaki Ichiba Abstract The C -terminal octapeptide of cholecystokinin (CCK8) includes some easily oxidizable amino acids. The oxidation of CCK8 by reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and hydroxyl radicals (OH,) was investigated using reversed-phase high performance liquid chromatography (RP-HPLC) and subsequent electrospray ionization mass spectrometry. The mechanism of oxidation of CCK8 in the H2O2 system differed from that of CCK8 in the Fenton system, in which OH, are produced. In the H2O2 system, 28Met and 31Met were oxidized to methionine sulfoxide, and no further oxidation or degradation/hydrolysis occurred. On the other hand, in the Fenton system, 28Met and 31Met residues were oxidized to methionine sulfone via the formation of methionine sulfoxide. In addition, the oxidized product was observed at the Trp residue but not at the Tyr residue, and small peptide fragments from CCK8 were observed in the Fenton system. From these results, it was concluded that 28Met and 31Met residues of CCK8 are susceptible to oxidation by ROS. Copyright © 2009 John Wiley & Sons, Ltd. [source] Minor histocompatibility antigens as targets for immunotherapy using allogeneic immune reactionsCANCER SCIENCE, Issue 8 2007Yoshiki Akatsuka Minor histocompatibility antigens (mHag) were originally identified as antigens causing graft rejection or graft-versus-host disease in human leukocyte antigen (HLA)-matched allogeneic transplantation. Molecular identification has revealed most to be major histocompatibility complex (MHC)-bound short peptide fragments encoded by genes which are polymorphic due to single nucleotide polymorphisms (SNP). Genotypic disparity of SNP between transplantation donors and recipients gives rise to mHag as non-self antigens for both the donor and the recipient. Subsequently, mHag have been explored as immunotherapeutic antigens for use against recurring hematological malignancies after allogeneic hematopoietic cell transplantation (HCT), because mHag expressed only on hematopoietic cells are considered to augment graft-versus-leukemia/lymphoma (GVL) effects without increasing the risk of life-threatening graft-versus-host disease (GVHD). Accumulating evidence suggests that T-cell responses to mHag aberrantly expressed on solid tumor cells are also involved in the eradication of sensitive tumors such as renal cell carcinomas following HCT. Over the past decade, the number of putative GVL-directed mHag has increased to a level that covers more than 30% of the Japanese patient population, so that clinical trials may now be executed in the setting of either vaccination or adoptive immunotherapy. As it is expected that immune responses to alloantigens are more powerful than to tumor antigens mostly derived from overexpressed self-proteins, mHag-based immunotherapy may lead to a new treatment modality for high-risk malignancies following allogeneic HCT. (Cancer Sci 2007; 98: 1139,1146) [source] From pro defensins to defensins: synthesis and characterization of human neutrophil pro ,-defensin-1 and its mature domainCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2003Z. Wu Abstract: Human neutrophil ,-defensins (HNPs) are small, cationic, Cys-rich antimicrobial proteins that play important roles in innate immunity against infectious microbes such as bacteria, fungi and enveloped viruses. Synthesized as inactive precursors in vivo (pre-proHNPs), HNPs are activated through proteolytic removal of the inhibitory pro-peptide required for subcellular sorting and correct folding. We seek to understand the molecular basis for the recognition between the 45-residue pro-peptide and the C-terminal functional domain. Here we described, total chemical synthesis of the 75-residue human neutrophil pro ,-defensin-1 (proHNP1) via native chemical ligation. After oxidative folding, proHNP1 is cleaved by cyanogen bromide at the Met45,Ala46 peptide bond to release the mature form. The native disulfide connectivity in HNP1, i.e. Cys1,Cys6, Cys2,Cys4 and Cys3,Cys5, is verified by mass mapping of peptide fragments generated by proteolytic digestion and Edman degradation. Fluorescence spectroscopy studies and antimicrobial activity assays further support that synthetic proHNP1 and HNP1 are correctly folded. While largely unstructured in aqueous solution, the pro-peptide binds to HNP1 intermolecularly with an apparent Kd value of 6.2 ,m at pH 7.4, confirming the mode of intramolecular inactivation of human ,-defensin precursors. [source] | ||||||||||||||||||||||||||||