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  • 1
  • 2
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 334-341 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 1.89 Å resolution structure of the complex of bovine pancreatic phospholipase A2 (PLA2) with the transition-state analogue L-1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine (TSA) has been determined. The crystal of the complex is trigonal, space group P3121, a = b = 46.58 and c = 102.91 Å and isomorphous to the native recombinant wild type (WT). The structure was refined to a final crystallographic R value of 18.0% including 957 protein atoms, 88 water molecules, one calcium ion and all 31 non-H atoms of the inhibitor at 1.89 Å resolution. In all, 7 726 reflections [F\gt2\sigma(F)] were used between 8.0 and 1.89 Å resolution. The inhibitor is deeply locked into the active-site cleft and coordinates to the calcium ion by displacing the two water molecules in the calcium pentagonal bipyramid by the anionic O atoms of the phosphate and phosphonate group. The hydroxyl group of Tyr69 hydrogen bonds to the second anionic O atom of the phosphate group while that of the phosphonate group replaces the third water, `catalytic' water, which forms a hydrogen bond to Nδ1 of His48. The fourth water which also shares Nδ1 of His48 is displaced by the steric hinderance of the inhibitor. The fifth conserved structural water is still present in the active site and forms a network of hydrogen bonds with the surrounding residues. The structure is compared with the other known TSA–PLA2 complexes.
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  • 4
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Members of the nuclear receptor (NR) superfamily of transcription factors modulate gene transcription in response to small lipophilic molecules. Transcriptional activity is regulated by ligands binding to the carboxy-terminal ligand-binding domains (LBDs) of cognate NRs. A subgroup of NRs ...
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  • 5
    ISSN: 1573-4986
    Keywords: cancer vaccines ; glycopeptides ; MUC-1 ; Immunotherapy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Translation of an immune response into therapy is probably the toughest task in designing vaccines for cancer due to the heterogeneity of the cell surface antigens which display tremendous variations in glycoforms. Consequently, a small segment (antigen) of the cancer-associated mucin, in spite of generating antigen-specific immune responses, may be limited in therapeutic value. It is important that the synthetic segment resembles the native cancer-associated mucin in both structure and conformation. Synthetic cancer associated mucin derived 16 amino acid peptide GVTSAPDTRAPAPGSTA and its partially glycosylated forms have demonstrated specific binding to two monoclonal antibodies, B27.29 and BCP8, raised against the native cancer associated mucin, MUC-1 and a MUC-1 derived synthetic peptide, respectively. In spite of the structural similarities at the core peptide level of both glycosylated and unglycosylated peptides, it appears that partial glycosylation does not inhibit and even slightly enhances binding to the MAb B27.29 indicating that the glycosylated synthetic peptide more closely resembles the native mucin epitope recognized by MAb B27.29. From molecular dynamic simulations using NMR derived distance constraints, both glycosylated and unglycosylated peptides have shown a type I β turn involving the same amino acids in both glycosylated and unglycosylated peptides. The αGalNAc attached to the threonine (T3) and serine (S4) in the 16 amino acid sequence has not imposed any conformational changes to the peptide backbone nor has offered severe steric resistance to the binding of either antibody to the glycopeptides as indicated by hapten inhibition studies. Nevertheless, all peptides have displayed glycosylation dependent specificities in binding to these antibodies, i.e. the glycosylated peptides demonstrated relative higher affinities to the native mucin antibody B27.29 while the unglycosylated peptide is more specific to the MAb BCP8. Immune responses generated by these synthetic glycopeptides are highly specific in recognizing the native cancer associated mucin.
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The importance of side-chain charge interactions in the formation of β-turns was studied. Sixteen protected NAc-tetrapeptide amides were studied, namely the variants of DEKS: NEKS, EEKS, DDKS, DQKS, NQKS, DERS, NERS, EERS, DDRS, NDRS, DQRS, and DKES. Three tetrapeptides - NPDM, NSDM, and NDDS - were also studied as they have a high probability of forming β-turns, based on statistical predictions. The results indicate that a small proportion of type I β-turn exists in solutions of DEKS and DERS in methanol/ water (60/40), while NEKS has an even smaller population of this turn. The other tetrapeptides are present in solution only in the extended conformation. These results clearly show the importance of the salt bridge between the side chains of K2 and E3 or R2 and E3, as well as the importance of the charge on the side chain of the first residue in stabilizing the β-turn. The relevance of statistical predictions for β-turns in short peptides is discussed.
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  • 7
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: CD and nmr studies have been carried out on aqueous trifluoroethanol (TFE) solutions of bradykinin (BK) and a bradykinin antagonist. The CD results exhibit a striking effect of TFE on the spectra of BK, with sequence Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg, and the BK antagonist, with sequence D-Arg-Arg-Pro-Hyp-Gly-Thi-D-Ser-D-Cpg-Cpg-Arg [where Hyp is 4-hydroxy-L-proline; Thi refers to β-(2-thienyl)-L-alanine and Cpg refers to α-cyclopentylglycine]. The effect of increasing concentration of TFE in water on the difference ellipticity at 222 nm was examined and showed that BK may be a mixture of at least two different conformers, one of which largely forms when the TFE concentration is increased beyond 80%. The linear extrapolation of 100% of the difference ellipticity of BK at low TFE concentrations yields a value in agreement with that shown by the BK antagonist, indicating that the conformation of BK at the lower TFE concentrations is similar to that of the BK antagonist. The conformational analysis was carried out using both one-dimensional and two-dimensional 1H-nmr techniques. The total correlation spectroscopy (TOCSY) spectrum of BK in a 60/40% (v/v) TFE/H2O solution at 10°C and a nuclear Overhauser effect spectroscopy (NOESY) spectrum that shows only sequential Hα(i) - NH(i + 1) or the Hα(i) - Hδδ′(i + 1) NOEs indicate that the majority of the molecules adopt an all-trans extended conformation. The TOCSY for BK in the 95/5% (v/v) TFE/H2O solution shows that there are two major conformations in the solution with about equal population. The NOESY experiment shows two new important cross peaks for one conformation, namely Pro2(α)-Pro3 (α) and the Pro2(α)-Gly4(NH), indicating a cis Pro2-Pro3 bond and a type VI β-turn between residues Arg1 and Gly4 involving cis proline at position 3, respectively. The low temperature coefficient of Gly4 for this conformation suggests the presence of an intramolecular hydrogen bond, therefore a type VIa β-turn is present. The other conformation is all trans and extended.The BK antafonist shows difference CD spectra in TFE solutions referred to H2O that are superficially indicative of a β-bend. However, nmr speaks against this possibility, as only one set of peaks were observed in the TOCSY and NOESY experiments, indicating an all-trans extended confirmation over the range of TFE concentrations. The BK-antagonist CD data suggest that solvent perturbation of the CD of an extended confirmation perturbation of the optical activity of the thienyl moiety of the peptide since the CD spectrum of N-acetyl-β-thienyl-L-alanine N-methylamide is strongly perturbed by TFE. The present results again demonstrate the complementary relationship between CD and nmr. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 1237-1247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Bradykinin (BK) is a peptide hormone with sequence Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9 and has been implicated in a multitude of pathophysiological processes such as the ability to lower systemic blood pressure and stimulate pain. BK analogues having bulky, β-branched D-aliphatic residues at position 7 combined with bulky L-aliphatic residues at position 8 have now been observed to be strong antagonists. Conformational studies based on two-dimensional nmr experiments in methanol/water (80/20 v/v) were carried out on several such active antagonists in a polar solvent. Included in this study were the very active antagonists, [D-Arg0, Hyp3, Thi5, D-Cpg7, Cpg8]-BK [Cpg: α-cyclo-pentyl-glycine; Hyp: trans-4-hydroxy-L-proline; Thi: β-(2-thienyl)-L-alanine] (I), [D-Arg0, Hyp3, D-Cpg7, Cpg8] -BK (II), as well as its variant with D-Cpg7 replaced by Cpg7, namely [D-Arg0, Hyp3, Cpg7, Cpg8]-BK (III). A turn-like structure, which coexists with the extended conformation, was observed between residues 2 and 5 for the most active antagonists I and II, in direct correlation with the peptide activities. No turn-like structure was found for residues 6-9. In peptide III, a turn-like structure was not identified. The existence of a turn at the C-terminal end of bradykinin and its analogues has been predicted by empirical calculations and supported by nmr measurements. But the present nmr study on the most active antagonists (I, II) does not support this hypothesis. Instead, the data suggest that a turn-like structure between residues 2 and 5 could be important for antagonist activity. Finally, one weak inhibitor [D-Cpg7]-BK (IV) showed no defined secondary structure. © 1993 John Wiley & Sons, Inc.
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  • 9
    Publication Date: 2018-03-05
    Description: Marine stratocumulus clouds cover nearly one-quarter of the ocean surface and thus play an extremely important role in determining the global radiative balance. The semipermanent marine stratocumulus deck over the southeastern Atlantic Ocean is of particular interest, because of its interactions with seasonal biomass burning aerosols that are emitted in southern Africa. Understanding the impacts of biomass burning aerosols on stratocumulus clouds and the implications for regional and global radiative balance is still very limited. Previous studies have focused on assessing the magnitude of the warming caused by solar scattering and absorption by biomass burning aerosols over stratocumulus (the direct radiative effect) or cloud adjustments to the direct radiative effect (the semidirect effect). Here, using a nested modeling approach in conjunction with observations from multiple satellites, we demonstrate that cloud condensation nuclei activated from biomass burning aerosols entrained into the stratocumulus (the microphysical effect) can play a dominant role in determining the total radiative forcing at the top of the atmosphere, compared with their direct and semidirect radiative effects. Biomass burning aerosols over the region and period with heavy loadings can cause a substantial cooling (daily mean −8.05 W m−2), primarily as a result of clouds brightening by reducing the cloud droplet size (the Twomey effect) and secondarily through modulating the diurnal cycle of cloud liquid water path and coverage (the cloud lifetime effect). Our results highlight the importance of realistically representing the interactions of stratocumulus with biomass burning aerosols in global climate models in this region.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2010-02-01
    Description: Little is known about the spatial variability in tree growth and its responses to climate on the Tibetan Plateau; however, such information is essential for improving predictions of forest ecosystem response to climatic change. A network of 16 ring width chronologies was developed along a latitudinal transect in the Qilian Mountains, northeastern Tibetan Plateau. A principal components analysis revealed that the residual chronologies had a positive loading on the first unrotated principal component (PC1). After rotation, PC1 yielded the highest loadings on the driest sites in the northwest and decreased to the south and to the east. PC2 was negatively correlated with altitude. Moisture availability was a dominant limiting factor for tree growth, and this dominance increased northwards and westwards along the precipitation gradient. Loadings of the first two rotated principal components separated the 16 forest sites into three major groups corresponding to the three regions affected by the East Asian Monsoon, Westerlies, and their interaction. Thus, spatial variability in tree growth is an excellent bioindicator of regional climate.
    Print ISSN: 0045-5067
    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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