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Peptide Molecules (peptide + molecule)
Selected AbstractsSMAP-29 has two LPS-binding sites and a central hingeFEBS JOURNAL, Issue 4 2002Brian F. Tack The CD spectra of SMAP-29, an antimicrobial peptide from sheep, showed disordered structure in aqueous buffers, and significant helicity in membrane-like environments, including SDS micelles, lipopolysaccharide (LPS) dispersions, and trifluoroethanol buffer systems. A structure determined by NMR in 40% perdeuterated trifluoroethanol indicated that residues 8,17 were helical, residues 18,19 formed a hinge, and residues 20,28 formed an ordered, hydrophobic segment. SMAP-29 was flexible in 40% trifluoroethanol, forming two sets of conformers that differed in the relative orientation of the N-terminal domain. We used a chromogenic Limulus assay to determine the EC50 of the peptide (the concentration that bound 50% of the added LPS). Studies with full-length and truncated SMAP-29 molecules revealed that each end of the holopeptide contained an LPS-binding domain. The higher affinity LPS-binding domain was situated in the flexible N-terminal portion. LPS binding to full-length SMAP-29 showed positive cooperativity, so the EC50 of the peptide (2.6 µm) was considerably lower than that of the individual LPS-binding domains. LPS-binding studies with a mixture of truncated peptides revealed that this cooperativity was primarily intramolecular (i.e. involving the N- and C-terminal LPS-binding sites of the same peptide molecule). CAP-18[106,142], an antimicrobial cathelicidin peptide of rabbits, resembled SMAP-29 in that it contained N- and C-terminal LPS-binding domains, had an EC50 of 2.5 µm, and bound LPS with positive cooperativity. We conclude that the presence of multiple binding sites that function cooperatively allow peptides such as SMAP-29 and CAP-18 to bind LPS with high affinity. [source] Isolation and characterisation of a partial peptide synthetase gene from Trichoderma asperellumFEMS MICROBIOLOGY LETTERS, Issue 2 2005Chanikul Chutrakul Abstract Many species of Trichoderma have attracted interest as agents for the biological control of soil borne fungal pathogens of a range of crop plants. Research on the biochemical mechanisms associated with this application has focused on the ability of these fungi to produce enzymes which lyse fungal cell walls, and antifungal antibiotics. An important group of the latter are the non-ribosomal peptides called peptaibols. In this study Trichoderma asperellum, a strain used in biological control in Malaysia, was found to produce the peptaibol, trichotoxin. This type of peptide molecule is synthesised by a peptide synthetase (PES) enzyme template encoded by a peptide synthetase (pes) gene. Using nucleotide sequences amplified from adenylation (A-) domains as probes, to hybridise against a , FIX®II genomic library from T. asperellum, 25 clones were recovered. These were subsequently identified as representative of four groups based on their encoding properties for specific amino acid incorporation modules in a PES. This was based on analysis of their amino acid sequences which showed up to 86% identity to other PESs including TEX 1. [source] Solid-phase synthesis of a dendritic peptide related to a retinoblastoma protein fragment utilizing a combined boc- and fmoc-chemistry approachJOURNAL OF PEPTIDE SCIENCE, Issue 5 2001Vittoria Cavallaro Abstract Dendritic peptides, often presented as multiple antigen peptides (MAPs), are widely used in immunological-based fields of research, although their synthesis can be extremely challenging. In this paper, a tetrameric dendritic MAP-like presentation of the retinoblastoma protein [649-654] sequence (4RB649-654) has been prepared using solid-phase peptide synthesis (SPPS) methods. During the synthesis of this dendritic molecule, numerous modifications to the synthetic protocols were examined. These modifications included the introduction of a combination Boc- and Fmoc-chemistry approach and also the use of 1,8-diazabicyclo[5.4.0]-undec-7-ene as a Fmoc-deprotection agent. The use in combination of Boc- and Fmoc-based synthetic strategies resulted in the production of the desired peptide molecule, 4RB649-654, in high purity and acceptable yields following purification by reversed phase HPLC. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] Mechanisms and modulation of intestinal epithelial repairINFLAMMATORY BOWEL DISEASES, Issue 1 2001Dr. Axel U. Dignass Abstract The mucosal epithelium of the alimentary tract represents a crucial barrier to a broad spectrum of noxious and immunogenic substances within the intestinal lumen. An impairment of the integrity of the mucosal epithelial barrier is observed in the course of various intestinal disorders including inflammatory bowel diseases (IBD), celiac disease, intestinal infections, and various other diseases. Furthermore, even under physiologic conditions temporary damage of the epithelial surface mucosa may be caused by proteases, residential flora, dietary compounds, or other factors. Generally, the integrity of the intestinal mucosal surface barrier is rapidly reestablished even after extensive destruction because of an enormous regenerative capability of the mucosal surface epithelium. Rapid resealing of the surface epithelium is accomplished by epithelial cell migration, also termed epithelial restitution, epithelial cell proliferation, and differentiation. Healing of the intestinal surface epithelium is regulated by a complex network of highly divergent factors, among them a broad spectrum of structurally distinct regulatory peptides that have been identified within the mucosa of the intestinal tract. These regulatory peptides, conventionally designated as growth factors and cytokines, play an essential role in regulating differential epithelial cell functions to preserve normal homeostasis and integrity of the intestinal mucosa. In addition, a number of other peptide molecules such as extracellular matrix factors and blood clotting factors, and also nonpeptide molecules including phospholipids, short-chain fatty acids, adenine nucleotides, trace elements, and pharmacological agents, have been demonstrated to modulate intestinal epithelial repair mechanisms. Some of these molecules may be released by platelets, adjacent stromal cells, inflammatory cells, or injured epithelial and nonepithelial cells and may play an important role in the modulation of intestinal injury. Repeated damage and injury of the intestinal surface are key features of various intestinal disorders including IBD and require constant repair of the epithelium. Enhancement of intestinal repair mechanisms by regulatory peptides or other modulatory factors may provide future approaches for the treatment of diseases that are characterized by injuries of the epithelial surface. [source] Dip-Pen Nanolithography of Bioactive Peptides on Collagen-Terminated Retinal Membrane,ADVANCED MATERIALS, Issue 19 2008Rizaldi Sistiabudi Dip-pen nanolithography is used to directly modify freshly dissected eye tissues with biologically active collagen-binding peptide molecules. The results address the challenge of surface heterogeneity and utilize dip-pen nanolithography to control the localization and concentration of molecules on a collagen-terminated tissue-derived surface. This method can allow the development of scaffolds for treatment of age-related macular degeneration. [source] Differential Expression of Vasoactive Intestinal Polypeptide Receptor 1 and 2 mRNA in Murine Intestinal T Lymphocyte SubtypesJOURNAL OF NEUROENDOCRINOLOGY, Issue 9 2001B.-F. Qian Abstract Neuropeptides may exert a variety of effects on the immune cells at both systemic and mucosal immune sites. The immunoregulatory properties refer to the ability of physiological signals and pathways to influence various immune functions. Vasoactive intestinal polypeptide (VIP), a neuropeptide present in high concentration in gut, was studied for its production and receptor expression in intraepithelial and lamina propria T lymphocytes of mouse intestine. Using reverse transcription-polymerase chain reaction (RT-PCR) analysis, it was demonstrated that VIP receptor 1 (VIPR1) was constantly expressed in intraepithelial and lamina propria T lymphocytes from both small and large intestine. In contrast, VIPR2 was identified only in T cells from small intestine. Further studies on purified subpopulations of T lymphocytes indicated the existence of VIPR2 in CD8+ T cells, but not CD4+ and CD4CD8 double negative T cells, although all these three subpopulations displayed VIPR1. In addition, VIPR1 mRNA was detected in splenic T lymphocytes, but no signal was obtained for VIPR2 mRNA, even after stimulation of the cells with anti-CD3,-chain mAb, phorbol 12-myristate 13-acetate (PMA) and/or VIP. The presence of VIP receptor(s) on intestinal T lymphocytes was supported by the detection of VIP on the cell surface using dual colour immunoflowcytometry. In-vitro treatment with VIP resulted in a tendency towards an increased size of the VIP immunoreactive T cell population and significantly enhanced the average immunofluorescence intensity of the surface labelling. This indicates that the receptors are partially occupied by locally produced VIP in vivo and that more peptide molecules can be bound on the lymphocytes when needed, released and accumulated in higher concentration at the action sites. We failed to detect the expression of VIP mRNA in T lymphocytes, from either intestine or spleen. These observations support that VIP may be an important immune modulator in gut acting through specific receptors on T lymphocytes. The differential mRNA expression of VIP receptor subtypes in cells with different phenotypes and in different immune compartments may suggest diverse regulatory roles of the neuropeptide in immune responses. [source] Metal ion-binding ability of tetrapeptides containing ,-aminoisobutyric acidJOURNAL OF PEPTIDE SCIENCE, Issue 3 2004Masayuki Hanyu Abstract ,-Aminoisobutyric acid (Aib), one of the C,, , -disubstituted glycines, is a sterically hindered amino acid that acts as a conformational constraint in peptides. However, studies for the application of the ability of Aib to control conformation are quite few. The paper focuses on the molecular recognition ability of acyclic oligopeptides containing Aib. Liquid,liquid extraction of nine kinds of metal ions from aqueous layers to nonpolar organic layers with acyclic tetrapeptides, X-Trp-Xaa2 -Gly-Xaa4 -NH-Ar (X = H or C6H5CH2OCO (Z), Xaa2 = Aib or Gly, Xaa4 = Leu or Ala, Ar = phenyl or 3,5-dimethylphenyl) was examined using picrate as the anion of ion pairs. The extraction behaviour of the metal ions with the tetrapeptides was investigated in the pH range from 3 to 9. In the case of basic pH regions, Cu(II) and Ag(I) were effectively extracted with Trp-Aib-Gly-Leu-NH-Ar. Pd(II) was specifically extracted with Trp-Aib-Gly-Leu-NH-Ar in acidic pH regions. The extraction percent (%E) of the peptide host, which has a 3,5-dimethylphenyl group, was even larger than that of the host, which has a phenyl group. Moreover, Pd(II) was extracted with a peptide host which has Leu and a 3,5-dimethylphenyl group in the absence of picrate as the anion of ion pairs. The free ,-amino group, the turn conformation and the hydrophobicity of peptide molecules were important factors for the extraction of the metals. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] l -Isoleucyl- l -asparagine 1.094-hydrate: a hybrid hydrogen-bonding patternACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Carl Henrik Görbitz The title compound, C10H20N3O4·1.094H2O, crystallizes with two dipeptide molecules in the asymmetric unit, each participating in two head-to-tail chains with hydrogen bonds between the terminal amino and carboxylate groups. As with many other dipeptides, the resulting structure is divided into distinct layers, but as the amide groups of the two peptide molecules participate in different types of interaction, the observed hydrogen bonds within a peptide main-chain layer (as distinct from the side-chain/solvent regions) cannot adapt to any of the four basic patterns observed previously for dipeptides. Instead, a rare hybrid pattern is formed. [source] Chiral interaction in peptide molecules: Effects of chiral peptide species on helix-sense induction in an N-terminal-free achiral peptideBIOPOLYMERS, Issue 5 2006Yoshihito Inai Abstract Noncovalent chiral domino effect (NCDE) has been proposed as terminal-specific interaction upon a 310 -helical peptide chain, of which the helix sense is manipulated by an external chiral stimulus (mainly amino acid derivatives) operating on the N-terminus (Inai, Y., et al. J Am Chem Soc 2000, 122, 11731,11732; ibid., 2002, 124, 2466,2473; ibid., 2003, 125, 8151,8162). We have investigated here a helix-sense induction in an optically inactive N-terminal-free nonapeptide (1) through the screening of several peptide species that differ in chiral sequence, chain length, and C-terminal group. Helix-sense induction in peptide 1 depends largely on both the C-terminal chirality and carboxyl group in the external peptide, in which N-carbonyl-blocked amino acids, "monopeptide acids," should be the minimum requirement for effective induction. N-Protected mono- to tetrapeptides of L -Leu residue commonly induce a right-handed helix. NMR study and theoretical computation reveal that the N-terminal segment of peptide 1 binds the N-protected dipeptide molecule through multipoint coordination to induce a right-handed helix preferentially. The present findings not only will improve our understanding of the chiral roles in peptide or protein helical termini, but also might demonstrate potential applications to chirality-responsive materials based on peptide helical fragments. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 471,481, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Specific Effects of Synthetic Oligopeptides on Cultured Animal Cells,BIOTECHNOLOGY PROGRESS, Issue 1 2002Franti, ek Fran Synthetic oligopeptides, tri- to pentaglycine and tri- and tetraalanine, were found to enhance viable cell density and culture viability when applied at concentrations higher than milllimolar to the cultures of a model hybridoma line. Oligoalanines, in addition, enhanced monoclonal antibody yields. Oligoglycines promoted solely the cell growth, unless the batch culture was fed with a medium concentrate. Examination of the effects of various tripeptides composed of glycine, alanine, serine, threonine, lysine, and histidine showed that some of the peptides promoted the growth of the culture, while other peptides suppressed the growth and enhanced the monoclonal antibody yield. Determination of the levels of amino acids and peptides in culture media indicated that the observed changes of culture parameters were caused by intact peptide molecules, rather than by amino acids liberated from the peptides by enzymic cleavage. [source] Computational study of conformational and chiroptical properties of (2R,3S,4R)-(+)-3,3,,4,4,,7-flavanpentolCHIRALITY, Issue 9 2005Chiara Cappelli Abstract Conformational analysis of (2R,3S,4R)-(+)-3,3,,4,4,,7-flavanpentol, a flavonoid compound displaying both antioxidant and pro-oxidant properties, is performed by molecular mechanics and density functional theory calculations both in the gas phase and in methanol solution by using the Polarizable Continuum Model. Nine different conformations are identified. Absorption (UV) and circular dichroism (CD) spectra and optical rotations are calculated by means of time dependent density functional theory (TDDFT) and compared with experiments. The effects of a complex environment formed by water and proline-rich peptide molecules on the conformational characteristics of (2R,3S,4R)-(+)-3,3,,4,4,,7-flavanpentol and therefore on its UV and CD spectra are investigated by atomistic molecular dynamics simulations. © 2005 Wiley-Liss, Inc. Chirality 17:577,589, 2005. [source] | ||||||||||||||||