| 16327900 |
Structure-activity relationship studies on CXCR4 antagonists having cyclic pentapeptide scaffolds |
10.1039/b513145f. |
Org Biomol Chem |
Structure-activity relationship studies on CXCR4 antagonists having cyclic pentapeptide scaffolds
Abstract
- Structure-activity relationship studies on CXCR4 antagonists, which were previously found by using cyclic pentapeptide libraries, were performed to optimize side-chain functional groups, involving conformationally constrained analogues. In addition, a new lead of cyclic pentapeptides with the introduction of a novel pharmacophore was developed.
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| 16335952 |
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry |
10.1021/pr0502065 |
Journal of proteome research |
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry
Abstract
- The enormous complexity, wide dynamic range of relative protein abundances of interest (over 10 orders of magnitude), and tremendous heterogeneity (due to post-translational modifications, such as glycosylation) of the human blood plasma proteome severely challenge the capabilities of existing analytical methodologies. Here, we describe an approach for broad analysis of human plasma N-glycoproteins using a combination of immunoaffinity subtraction and glycoprotein capture to reduce both the protein concentration range and the overall sample complexity. Six high-abundance plasma proteins were simultaneously removed using a pre-packed, immobilized antibody column. N-linked glycoproteins were then captured from the depleted plasma using hydrazide resin and enzymatically digested, and the bound N-linked glycopeptides were released using peptide-N-glycosidase F (PNGase F). Following strong cation exchange (SCX) fractionation, the deglycosylated peptides were analyzed by reversed-phase capillary liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Using stringent criteria, a total of 2053 different N-glycopeptides were confidently identified, covering 303 nonredundant N-glycoproteins. This enrichment strategy significantly improved detection and enabled identification of a number of low-abundance proteins, exemplified by interleukin-1 receptor antagonist protein (approximately 200 pg/mL), cathepsin L (approximately 1 ng/mL), and transforming growth factor beta 1 (approximately 2 ng/mL). A total of 639 N-glycosylation sites were identified, and the overall high accuracy of these glycosylation site assignments as assessed by accurate mass measurement using high-resolution liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) is initially demonstrated.
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| 16372000 |
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae |
10.1038/nature04341. |
Nature |
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
Abstract
- The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.
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| 16372009 |
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus |
10.1038/nature04332. |
Nature |
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
Abstract
- Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.
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| 16387709 |
Novel peptides of therapeutic promise from Indian Conidae |
10.1196/annals.1352.022. |
Ann N Y Acad Sci |
Novel peptides of therapeutic promise from Indian Conidae
Abstract
- Highly structured small peptides are the major toxic constituents of the venom of cone snails, a family of widely distributed predatory marine molluscs. These animals use the venom for rapid prey immobilization. The peptide components in the venom target a wide variety of membrane-bound ion channels and receptors. Many have been found to be highly selective for a diverse range of mammalian ion channels and receptors associated with pain-signaling pathways. Their small size, structural stability, and target specificity make them attractive pharmacologic agents. A select number of laboratories mainly from the United States, Europe, Australia, Israel, and China have been engaged in intense drug discovery programs based on peptides from a few snail species. Coastal India has an estimated 20-30% of the known cone species; however, few serious studies have been reported so far. We have begun a comprehensive program for the identification and characterization of peptides from cone snails found in Indian Coastal waters. This presentation reviews our progress over the last 2 years. As expected from the evolutionary history of these venom components, our search has yielded novel peptides of therapeutic promise from the new species that we have studied.
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| 16389447 |
Key role of glutamic acid for the cytotoxic activity of the cyclotide cycloviolacin O2 |
10.1007/s00018-005-5486-4. |
Cell Mol Life Sci |
Key role of glutamic acid for the cytotoxic activity of the cyclotide cycloviolacin O2
Abstract
- Cyclotides are cyclic plant proteins with potent cytotoxic effects. Here we systematically probed the importance of surface-exposed charged amino acid residues of the cyclotide cycloviolacin O2, using a strategy involving chemical modifications. We show that the single glutamic acid plays a key role for the cytotoxicity: methylation of this residue produced a 48-fold decrease in potency. Virtually no change in potency was observed when masking the single arginine residue using 1,2-cyclohexanedione, while acetylation of the two lysine residues reduced the potency 3-fold. The derivative with modifications at both arginine and lysine residues showed a 7-fold loss of potency. In addition, we show that the activity is dependent on an intact disulfide network and that the short sequences between the six cysteine residues, that is, the backbone loops, are devoid of cytotoxic activity.
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| 16394170 |
Skin secretions of Rana saharica frogs reveal antimicrobial peptides esculentins-1 and -1B and brevinins-1E and -2EC with novel insulin releasing activity |
10.1677/joe.1.06293. |
J Endocrinol |
Skin secretions of Rana saharica frogs reveal antimicrobial peptides esculentins-1 and -1B and brevinins-1E and -2EC with novel insulin releasing activity
Abstract
- Skin secretions of Rana saharica were evaluated for the isolation and characterisation of novel insulinotropic peptides. Crude secretions obtained from young adult frogs by mild electrical stimulation of the dorsal skin surface were purified by reverse phase HPLC yielding 80 fractions. In acute 20-min incubations with glucose responsive BRIN-BD11 cells, fractions 36-43, 46-54 and 57-63 significantly stimulated insulin release by 2- to 8-fold compared with 5.6 mM glucose alone. Pooled fractions in the latter two bands were rechromatographed to reveal 9 homogenous peaks, which elicited significant 1.3- to 3.5-fold increases in insulin release (P < 0.05). Structural analysis of the most potent non-toxic peptides was performed by mass spectrometry and automated Edman degradation. This revealed four major insulin-releasing peaks with molecular masses of 2,676.9 Da, 3,519.3 Da, 4,920.4 Da and 4,801.2 Da respectively. These peptides were found to be identical to brevinin-1E, brevinin-2EC, esculentin-1 and esculentin-1B, which belong to the group of antimicrobial peptides isolated from skin secretions of various Rana frog species. Preliminary studies on the mechanism underlying the insulinotropic actions of esculentins-1 and -1B suggested possible involvement of both cyclic AMP-protein kinase A and -C-dependent G-protein sensitive pathways. These data indicate that the skin secretions of Rana saharica frogs contain bioactive molecules with significant insulin-releasing activity. Relatives of the brevinin/esculentin peptide family merit further investigation as novel insulin secretagogues.
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| 16413829 |
Antimicrobial peptides from the skin of the Tsushima brown frog Rana tsushimensis |
10.1016/j.cbpc.2005.11.022. |
Comp Biochem Physiol C Toxicol Pharmacol |
Antimicrobial peptides from the skin of the Tsushima brown frog Rana tsushimensis
Abstract
- The Tsushima brown frog Rana tsushimensis Stejneger, 1907 exists in reproductive isolation on the island of Tsushima, Japan. Six peptides with antimicrobial activity were isolated in pure form from an extract of the skin of this species and their amino acid sequences identified them as members of the brevinin-1 (one peptide), brevinin-2 (one peptide) and temporin (four peptides) families. The C-terminally alpha-amidated brevinin-1 peptide (FLGSIVGALASALPSLISKIRN.NH2) lacks the cyclic heptapeptide domain Cys18-(Xaa)4-Lys-Cys24 at the COOH-terminus of the molecule that characterizes other members of that family. A structurally similar brevinin-1 peptide, also lacking the cyclic domain, was previously isolated from the skin of the Ryukyu brown frog Rana okinavana, indicative of a close phylogenetic relationship between the species. Brevinin-2TSa (GIMSLFKGVLKTAGKHVAGSLVDQLKCKITGGC) showed broad-spectrum growth inhibitory activity against a range of Gram-negative and Gram-positive bacteria (including methicillin-resistant Staphylococcus aureus) (minimum inhibitory concentrations< or =25 microM) and relatively low hemolytic activity against human erythrocytes (LD50=100 microM). The peptide therefore represents a candidate for drug development.
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| 16427248 |
Cloning from tissue surrogates: antimicrobial peptide (esculentin) cDNAs from the defensive skin secretions of Chinese ranid frogs |
10.1016/j.ygeno.2005.12.002. |
Genomics |
Cloning from tissue surrogates: antimicrobial peptide (esculentin) cDNAs from the defensive skin secretions of Chinese ranid frogs
Abstract
- The defensive skin secretions of amphibians are a rich source of bioactive peptides. Here we describe a rapid technique for skin granular gland transcriptome cloning from a surrogate tissue-the secretion itself. cDNA libraries were constructed from lyophilized skin secretion from each of the Chinese frogs (Rana schmackeri, Rana versabilis, and Rana plancyi fukienensis) using magnetic oligo(dT) bead-captured polyadenylated mRNA as templates. Specific esculentin cDNAs were amplified by 3'-RACE using a degenerate primer designed for a consensus nucleotide sequence in the 5' untranslated region of previously characterized ranid frog peptide cDNAs. The cloned cDNAs were found to encode the antimicrobial peptides esculentins 1 and 2 from each of the species examined. The presence of predicted peptide structures in skin secretions was confirmed by MALDI-TOF mass spectrometry and automated Edman degradation. This experimental approach can thus rapidly expedite parallel transcriptome and peptidome analysis of amphibian granular gland secretions without harming or sacrificing donor animals.
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| 16441062 |
Cycloviolacin H4, a hydrophobic cyclotide from Viola hederaceae |
10.1021/np050317i. |
J Nat Prod |
Cycloviolacin H4, a hydrophobic cyclotide from Viola hederaceae
Abstract
- Cycloviolacin H4, a new macrocyclic miniprotein comprising 30 amino acid residues, was isolated from the underground parts of the Australian native violet Viola hederaceae. Its sequence, cyclo-(CAESCVWIPCTVTALLGCSCSNNVCYNGIP), was determined by nanospray tandem mass spectrometry and quantitative amino acid analysis. A knotted disulfide arrangement, which was designated as a cyclic cystine knot motif and characteristic to all known cyclotides, is proposed for stabilizing the molecular structure and folding. The cyclotide is classified in the bracelet subfamily of cyclotides due to the absence of a cis-Pro peptide bond in the circular peptide backbone. A model of its three-dimensional structure was derived based on the template of the homologous cyclotide vhr1 (Trabi et al. Plant Cell 2004, 16, 2204-2216). Cycloviolacin H4 exhibits the most potent hemolytic activity in cyclotides reported so far, and this activity correlates with the size of a surface-exposed hydrophobic patch. This work has thus provided insight into the factors that modulate the cytotoxic properties of cyclotides.
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| 16442634 |
Determination of microcystins in environmental samples using capillary electrophoresis |
10.1016/j.jbbm.2005.12.002. |
J Biochem Biophys Methods |
Determination of microcystins in environmental samples using capillary electrophoresis
Abstract
- The applicability of capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) methods for the simultaneous determination of two frequently occurring microcystins (MCs-LR and -YR) and a new variant (MC-YA) in crude extracts of Hungarian bloom samples and cyanobacterial cultures was studied. It was found that the comparison of the results obtained by both CZE and MEKC measurements (due to the differences in their separation mechanisms) for the same sample can guarantee the reliability of the quantitative results. In our work environmental samples like lake waters, water bloom samples, cyanobacterial isolates were analysed. The three microcystins could be directly determined in water bloom samples collected from Hungarian lakes and laboratory culture samples of cyanobacteria.
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| 16457628 |
Solid-phase synthesis in the twenty-first century |
10.2174/138955706775197866. |
Mini Rev Med Chem |
Solid-phase synthesis in the twenty-first century
Abstract
- Solid-phase synthesis is a powerful tool for achieving high-throughput chemistry. This review discusses recent diverse examples from my group: the solid-phase synthesis of unsymmetrical guanidines, polymer-supported versions of cyclooctadiene and 9-BBN, a triflate-like linker, the synthesis of tetrahydro-beta-carbolines by the acyliminium Pictet-Spengler reaction, and a total synthesis of the antimycobacterial cyclic depsipeptide natural product kahalalide A.
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| 16457862 |
Two novel O-superfamily conotoxins from Conus vexillum |
10.1016/j.toxicon.2005.12.007. |
Toxicon |
Two novel O-superfamily conotoxins from Conus vexillum
Abstract
- O-superfamily conotoxins include several families that have diverse pharmacological activity on Na+, K+ or Ca2+ channels. These superfamily toxins have been mainly found in fish-hunting and mollusk-hunting Conus species. Here, we reported two novel O-superfamily conotoxins, vx6a and vx6b, purified from a worm-hunting cone snail, Conus vexillum. Though their cysteine framework and signal peptides share high similarity with those of other members of O-superfamily, the mature vx6a and vx6b both have a low sequence homology with others. To test the biological function of vx6a, the toxin was chemically synthesized and then tested on the locust dorsal unpaired median (DUM) neuron system which containing various ion channels. Although no any activity on ion channels was found on the DUM neuron system, vx6a could clearly elicit a series of symptoms in mouse via intracranial injection, such as quivering, climbing, scratching, barrel rolling and paralysis of limbs at different dose.
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| 16459058 |
Identification of three novel ostricacins: an update on the phylogenetic perspective of beta-defensins |
10.1016/j.ijantimicag.2005.10.013. |
Int J Antimicrob Agents |
Identification of three novel ostricacins: an update on the phylogenetic perspective of beta-defensins
Abstract
- Three new beta-defensins, ostricacins-2, 3 and 4 (Osp-2, 3 and 4), have been successfully purified and characterised from ostrich heterophils in addition to ostricacin-1 (Osp-1). These peptides are composed of 36-42 amino acids with a molecular weight range of 4.70-4.98 kDa. In vitro, Osp-1, 3 and 4 were active against Escherichia coli O157:H7 and Staphylococcus aureus 1056 MRSA, whilst Osp-2 was active against bacterial strains plus the yeast Candida albicans 3153A. Minimal inhibitory concentrations of the three ostricacins ranged from 0.96 microg/mL to 12.03 microg/mL. Comparison with the known beta-defensins from mammalian and other avian species revealed that the four ostricacins shared eight conserved residues (six cysteines and two glycines), identified as the 'beta-defensin core motif'. Comparisons of the sequence also indicated that beta-defensins could have originated from a common beta-defensin-like ancestor that occurred before avian and mammalian lines diverged.
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| 16461661 |
Molecular and genetic characterization of a novel nisin variant produced by Streptococcus uberis |
10.1128/AEM.72.2.1148-1156.2006. |
Appl Environ Microbiol |
Molecular and genetic characterization of a novel nisin variant produced by Streptococcus uberis
Abstract
- Streptococcus uberis is one of the principal causative agents of bovine mastitis. In this study, we report that S. uberis strain 42 produces a lantibiotic, nisin U, which is 78% identical (82% similar) to nisin A from Lactococcus lactis. The 15.6-kb nisin U locus comprises 11 open reading frames, similar in putative functionality but differing in arrangement from that of the nisin A biosynthetic cluster. The nisin U producer strain exhibits specific resistance (immunity) to nisin U and cross-resistance to nisin A, a finding consistent with the 55% sequence similarity of their respective immunity peptides. Homologues of the nisin U structural gene were identified in several additional S. uberis strains, and in each case cross-protective immunity was expressed to nisin A and to the other producers of nisin U and its variants. To our knowledge, this is the first report both of characterization of a bacteriocin by S. uberis, as well as of a member of the nisin family of peptides in a species other than L. lactis.
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