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Helix Formation (helix + formation)
Selected AbstractsSynthesis of 3,,3,-Linked Pyrimidine Oligonucleotides Containing an Acridine Moiety for Alternate Strand Triple Helix FormationEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 11 2004Jussara Amato Abstract Oligonucleotides with a 3,,3, inversion of polarity, containing an acridine moiety attached to the nucleotide base flanking the 3,,3, phosphodiester bond, have been synthesised, characterised and used to form alternate-strand triple helix complexes. These have been investigated by UV melting studies and CD experiments. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Surfactant-Induced Helix Formation of Cylindrical Brush Polymers with Poly(L -lysine) Side ChainsMACROMOLECULAR RAPID COMMUNICATIONS, Issue 10 2008Nikhil Gunari Abstract The complex formation of oppositely charged surfactants with some polypeptides is known to induce , -sheet or helix formation. Here, we report on the complex formation of cylindrical brush polymers with poly(L -lysine) side chains and sodium dodecylsulfate (SDS). With increasing amount of added surfactant the cylindrical polymers first adopt a helical conformation with a pitch of approximately 14,24 nm followed by a spherically collapsed structure before eventually precipitation occurs. CD measurements suggest that the helix formation of the cylindrical brush polymers is driven by the hydrophobicity of the , -sheets formed by the PLL side chain,SDS complexes. [source] Helix Formation in Synthetic Polymers by Hydrogen Bonding with Native Saccharides in Protic MediaCHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2006Minoru Waki Abstract Water-soluble poly(m -ethynylpyridine)s were designed to realize saccharide recognition in protic media. UV/Vis, 1H NMR, and fluorescence measurements revealed that the polymer forms a helical higher order structure by solvophobic interactions between the ethynylpyridine units in the protic medium. The resulting pore in the helix behaves like a binding pocket in proteins, by taking advantage of inwardly directed hydrogen-bonding functional groups of the polymers. Molecular recognition of native saccharides by the polymers was investigated by circular dichroism (CD). The chirality of the saccharide was transferred to the helical sense of the polymers, accompanied by the appearance of induced CDs (ICDs) in the absorptive region of the polymers. In MeOH/water (10/1), mannose and allose showed intense ICDs, and the apparent association constant between the polymer and D -mannose was 14,M,1. [source] Domain V of m-calpain shows the potential to form an oblique-orientated ,-helix, which may modulate the enzyme's activity via interactions with anionic lipidFEBS JOURNAL, Issue 22 2002Klaus Brandenburg The activity of m-calpain, a heterodimeric, Ca2+ -dependent cysteine protease appears to be modulated by membrane interactions involving oblique-orientated ,-helix formation by a segment, GTAMRILGGVI, in the protein's smaller subunit. Here, graphical and hydrophobic moment-based analyses predicted that this segment may form an ,-helix with strong structural resemblance to the influenza virus peptide, HA2, a known oblique-orientated ,-helix former. Fourier transform infrared spectroscopy showed that a peptide homologue of the GTAMRILGGVI segment, VP1, adopted low levels of ,-helical structure (, 20%) in the presence of zwitterionic lipid and induced a minor decrease (3 °C) in the gel to liquid-crystalline phase transition temperature, TC, of the hydrocarbon chains of zwitterionic membranes, suggesting interaction with the lipid headgroup region. In contrast, VP1 adopted high levels of ,-helical structure (65%) in the presence of anionic lipid, induced a large increase (10 °C) in the TC of anionic membranes, and showed high levels of anionic lipid monolayer penetration (,SP = 5.5 mN·m,1), suggesting deep levels of membrane penetration. VP1 showed strong haemolytic ability (LD50 = 1.45 mm), but in the presence of ionic agents, this ability, and that of VP1 to penetrate anionic lipid monolayers, was greatly reduced. In combination, our results suggest that m-calpain domain V may penetrate membranes via the adoption of an oblique-orientated ,-helix and electrostatic interactions. We speculate that these interactions may involve snorkelling by an arginine residue located in the polar face of this ,-helix. [source] Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital methodINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2009Toshihiko Sawada Abstract The fragment molecular orbital method (FMO) was applied to the geometry optimization of several heparin oligosaccharides at the RHF/6-31(+)G(d) level combined with the polarizable continuum model (PCM). For comparison, GLYCAM force field optimization in explicit solvent was also conducted. Good accuracy of FMO was demonstrated in comparison to ab initio at the MP2/PCM level. The interaction analysis was conducted using the pair interaction energy decomposition analysis (PIEDA), and the role of hydrogen bonding and solvent was elucidated in the helix formation of heparin in solution. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solventJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2007Anna Jagielska Abstract The influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all-atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007 [source] The conformation of fusogenic B18 peptide in surfactant solutions,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Sandra Rocha Abstract The interaction of B18 peptide with surfactants has been studied by circular dichroism spectroscopy and fluorescence measurements. B18 is the fusogenic motif of the fertilization sea urchin protein. The peptide forms an ,-helix structure when interacting with positively or negatively charged surfactants below and above the critical micellar concentration (CMC). The ,-helix formation is due to binding of surfactant monomers rather than the formation of surfactant micelles on the peptide. Fluorescence measurements show that the CMC of the negatively charged surfactant increases in the presence of B18, supporting the fact that there is a strong interaction between the peptide and monomers. Nonionic surfactant monomers have no effect on the peptide structure, whereas the micelles induce an ,-helical conformation. In this case the helix stabilization results from the formation of surfactant micelles on the peptide. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Collagen-like triple helix formation of synthetic (Pro-Pro-Gly)10 analogues: (4(S)-hydroxyprolyl-4(R)-hydroxyprolyl-Gly)10, (4(R)-hydroxyprolyl-4(R)-hydroxyprolyl-Gly)10 and (4(S)-fluoroprolyl-4(R)-fluoroprolyl-Gly)10JOURNAL OF PEPTIDE SCIENCE, Issue 10 2005Masamitsu Doi Abstract For the rational design of a stable collagen triple helix according to the conventional rule that the pyrrolidine puckerings of Pro, 4-hydroxyproline (Hyp) and 4-fluoroproline (fPro) should be down at the X-position and up at the Y-position in the X-Y-Gly repeated sequence for enhancing the triple helix propensities of collagen model peptides, a series of peptides were prepared in which X- and Y-positions were altogether occupied by HypR, HypS, fProR or fProS. Contrary to our presumption that inducing the X-Y residues to adopt a down-up conformation would result in an increase in the thermal stability of peptides, the triple helices of (HypS -HypR -Gly)10 and (fProS -fProR -Gly)10 were less stable than those of (Pro-HypR -Gly)10 and (Pro-fProR -Gly)10, respectively. As reported by Bächinger's and Zagari's groups, (HypR -HypR -Gly)10 which could have an up-up conformation unfavorable for the triple helix, formed a triple helix that has a high thermal stability close to that of (Pro-HypR -Gly)10. These results clearly show that the empirical rule based on the conformational preference of pyrrolidine ring at each of X and Y residues should not be regarded as still valid, at least for predicting the stability of collagen models in which both X and Y residues have electronegative groups at the 4-position. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and chiroptical properties of optically active poly(ethynylcarbazole) derivatives: Substituent effect on the helix formationJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 19 2007Fumio Sanda Abstract Novel chiral acetylene monomers containing carbazole, 2-ethynyl-9-[(S)-2-methylbutoxycarbonyl]carbazole (1), 3-ethynyl-9-[(S)-2-methylbutoxycarbonyl]carbazole (2), 2-ethynyl-9-[(S)-2-methylbutyl]carbazole (3), and 2-ethynyl-9-[(S)-4-methylhexyl]carbazole (4) were synthesized and polymerized with [(nbd)RhCl]2Et3N. The corresponding polyacetylenes with number-average molecular weights ranging from 68,700 to 310,000 were obtained in good yields. Poly(1) exhibited a large specific rotation and an intense Cotton effect in toluene, indicating that it formed a helix with predominantly one-handed screw sense, while the other three polymers showed no evidence for taking a helical structure. Poly(1) largely decreased the CD intensity upon heating from ,10 to 60 °C. Poly(1) showed a Cotton effect in film state in a manner similar to solution state. No chiral amplification was observed in the copolymerization of 1 with achiral 2-ethynyl-9- tert -butoxycarbonylcarbazole (5). © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4450,4458, 2007 [source] Surfactant-Induced Helix Formation of Cylindrical Brush Polymers with Poly(L -lysine) Side ChainsMACROMOLECULAR RAPID COMMUNICATIONS, Issue 10 2008Nikhil Gunari Abstract The complex formation of oppositely charged surfactants with some polypeptides is known to induce , -sheet or helix formation. Here, we report on the complex formation of cylindrical brush polymers with poly(L -lysine) side chains and sodium dodecylsulfate (SDS). With increasing amount of added surfactant the cylindrical polymers first adopt a helical conformation with a pitch of approximately 14,24 nm followed by a spherically collapsed structure before eventually precipitation occurs. CD measurements suggest that the helix formation of the cylindrical brush polymers is driven by the hydrophobicity of the , -sheets formed by the PLL side chain,SDS complexes. [source] Fractionation of transgenic corn seed by dry and wet milling to recover recombinant collagen-related proteinsBIOTECHNOLOGY PROGRESS, Issue 5 2009Cheng Zhang Abstract Corn continues to be considered an attractive transgenic host for producing recombinant therapeutic and industrial proteins because of its potential for producing recombinant proteins at large volume and low cost as coproducts of corn seed-based biorefining. Efforts to reduce production costs have been primarily devoted to increasing accumulation level, optimizing protein extraction conditions, and simplifying the purification. In the present work, we evaluated two grain fractionation methods, dry milling and wet milling, to enrich two recombinant collagen-related proteins; thereby, reducing the amount and type of corn-derived impurities in subsequent protein extraction and purification steps. The two proteins were a full-length human recombinant collagen type I alpha 1(rCI,1) chain with telopeptides and peptide foldon to effect triple helix formation and a 44-kDa rCI,1 fragment. For each, ,60% of the rCI,1s in the seed was recovered in the dry-milled germ-rich fractions making up ca. 25% of the total kernel mass. For wet milling, ,60% of each was recovered in three fractions accounting for 20,25% of the total kernel mass. The rCI,1s in the dry-milled germ-rich fractions were enriched three to six times compared with the whole corn kernel, whereas the rCI,1s were enriched 4,10 times in selected wet-milled fractions. The recovered starch from wet milling was almost free of rCI,1. Therefore, it was possible to generate rCI,1-enriched fractions by both dry and wet milling along with rCI,1-free starch using wet milling. Because of its simplicity, the dry milling procedure could be accomplished on-farm thus minimizing the risk of inadvertent release of viable transgenic seeds. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Templated assembly of the pH-sensitive membrane-lytic peptide GALACHEMICAL BIOLOGY & DRUG DESIGN, Issue 6 2004D.H. Haas Abstract:, Delivery of protein or nucleic acid therapeutics into intracellular compartments may require facilitation to allow these macromolecules to cross otherwise impermeant cellular membranes. Peptides capable of forming membrane-spanning channels hold promise as just such facilitators, although the requirement for peptide oligomerization to form these channels may limit their effectiveness. Synthetic molecules containing multiple copies of membrane-active peptides attached to a template molecule in a pre-oligomerized form have attracted interest for drug-delivery applications. Using three template designs, we synthesized multimeric versions of the pH-sensitive lytic peptide GALA and compared their performance to monomeric GALA. Template assembly stabilized helix formation: templated GALA retained , -helical structure even at neutral pH, unlike monomeric GALA. In membrane leakage assays, templated GALA retained the pH sensitivity of the monomer, with improved leakage for dimeric GALA. Surprisingly, trimeric GALA was less effective, particularly when synthesized with a larger and more flexible spacer. Surface plasmon resonance analysis indicated that reversible binding of templated GALA to lipid surfaces at acidic conditions was greatly reduced compared with monomeric GALA, but that the amount of irreversibly bound material was similar. We interpreted these results to indicate that templated peptides may cyclize into ,self-satisfied' oligomeric structures, incapable of further aggregation and subsequent pore formation. Future design of templated peptides must be carefully performed to avoid this unwanted consequence. [source] | ||||||||||||||||