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  • Biochemistry  (1,848)
  • Wiley-Blackwell  (1,822)
  • Springer  (26)
  • Nature Publishing Group
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  • 1
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    Springer Nature | Springer
    Publication Date: 2024-04-14
    Description: This open access book highlights concepts discussed at two international conferences that brought together world-renowned scientists to advance the science of potassium (K) recommendations for crops. There was general agreement that the potassium recommendations currently in general use are oversimplified, outdated, and jeopardize soil, plant, and human health. Accordingly, this book puts forward a significantly expanded K cycle that more accurately depicts K inputs, losses and transformations in soils. This new cycle serves as both the conceptual basis for the scientific discussions in this book and a framework upon which to build future improvements. Previously used approaches are critically reviewed and assessed, not only for their relevance to future enhancements, but also for their use as metrics of sustainability. An initial effort is made to link K nutrition in crops and K nutrition in humans. The book offers an invaluable asset for graduate students, educators, industry scientists, data scientists, and advanced agronomists.
    Keywords: Agriculture ; Plant Biochemistry ; Soil Science & Conservation ; Applied Ecology ; Soil Science ; Bioavailable Potassium ; Fertilizer Management ; Plant Nutrition ; Potash ; Soil Chemistry ; Sustainability ; Open access ; Agricultural science ; Botany & plant sciences ; Biochemistry ; Sedimentology & pedology ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TV Agriculture and farming::TVB Agricultural science ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RB Earth sciences::RBG Geology, geomorphology and the lithosphere::RBGB Sedimentology and pedology ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment::RNC Applied ecology
    Language: English
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  • 2
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    Springer Nature | Springer
    Publication Date: 2024-04-14
    Description: This book is open access under a CC BY 4.0 license. By 2050, human population is expected to reach 9.7 billion. The demand for increased food production needs to be met from ever reducing resources of land, water and other environmental constraints. Rice remains the staple food source for a majority of the global populations, but especially in Asia where ninety percent of rice is grown and consumed. Climate change continues to impose abiotic and biotic stresses that curtail rice quality and yields. Researchers have been challenged to provide innovative solutions to maintain, or even increase, rice production. Amongst them, the ‘green super rice’ breeding strategy has been successful for leading the development and release of multiple abiotic and biotic stress tolerant rice varieties. Recent advances in plant molecular biology and biotechnologies have led to the identification of stress responsive genes and signaling pathways, which open up new paradigms to augment rice productivity. Accordingly, transcription factors, protein kinases and enzymes for generating protective metabolites and proteins all contribute to an intricate network of events that guard and maintain cellular integrity. In addition, various quantitative trait loci associated with elevated stress tolerance have been cloned, resulting in the detection of novel genes for biotic and abiotic stress resistance. Mechanistic understanding of the genetic basis of traits, such as N and P use, is allowing rice researchers to engineer nutrient-efficient rice varieties, which would result in higher yields with lower inputs. Likewise, the research in micronutrients biosynthesis opens doors to genetic engineering of metabolic pathways to enhance micronutrients production. With third generation sequencing techniques on the horizon, exciting progress can be expected to vastly improve molecular markers for gene-trait associations forecast with increasing accuracy. This book emphasizes on the areas of rice science that attempt to overcome the foremost limitations in rice production. Our intention is to highlight research advances in the fields of physiology, molecular breeding and genetics, with a special focus on increasing productivity, improving biotic and abiotic stress tolerance and nutritional quality of rice. ; Up-to-date contributions by experts from international research centers and universities Provides practical knowledge and strong scientific foundation on rice biotechnology All-in-one resource for current advances in rice breeding Open Access
    Keywords: Agriculture ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Plant Physiology ; Nutrition ; Plant Biotechnology ; Plant Genetics ; Open Access ; Rice Biotechnologies ; Rice Breeding ; biotic stress tolerance ; abiotic stress tolerance ; Submergence tolerance ; Biofortification ; Marker Assisted and Forward Breeding ; disease resistance ; CRISPR/CAS ; Agricultural science ; Botany & plant sciences ; Biotechnology ; Genetics (non-medical) ; Biochemistry ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TV Agriculture and farming::TVB Agricultural science ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 3
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    Springer Nature | Springer
    Publication Date: 2024-04-11
    Description: This open access book reports on a pilot project aiming at collecting information on the socio-ecological risks that could arise in the event of an uncontrolled spread of genetically engineered organisms into the environment. The researchers will, for instance, be taking a closer look at genetically engineered oilseed rape, genetically engineered olive flies as well as plants and animals with so-called gene drives. The book mainly adresses researchers.
    Keywords: Ecotoxicology ; Environmental Health ; Environmental Management ; Genetically modified organisms ; Socio-ecological risk ; Olive flies ; Environmental spread ; Open Access book ; Environmental science, engineering & technology ; Biochemistry ; Environmental medicine ; Environmental management, ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TQ Environmental science, engineering and technology ; thema EDItEUR::M Medicine and Nursing::MK Medical specialties, branches of medicine::MKV Environmental medicine ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment::RNF Environmental management
    Language: English
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  • 4
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers a comprehensive overview of the role and potential of microorganisms in the degradation and preservation of cultural materials (e.g. stone, metals, graphic documents, textiles, paintings, glass, etc.). Microorganisms are a major cause of deterioration in cultural artefacts, both in the case of outdoor monuments and archaeological finds. This book covers the microorganisms involved in biodeterioration and control methods used to reduce their impact on cultural artefacts. Additionally, the reader will learn more about how microorganisms can be used for the preservation and protection of cultural artefacts through bio-based and eco-friendly materials. New avenues for developing methods and materials for the conservation of cultural artefacts are discussed, together with concrete advances in terms of sustainability, effectiveness and toxicity, making the book essential reading for anyone interested in microbiology and the preservation of cultural heritage.
    Keywords: Microbiology ; Cultural Heritage ; Microbial Ecology ; Microbial Genetics and Genomics ; Enzymology ; Applied Microbiology ; Microbial Genetics ; Industrial Microbiology ; Open Access ; Restoration ; Conservation ; Biodeterioration ; Bioweathering ; Bioremediation ; Biocleaning ; Biotechnology ; Green Chemistry ; Fungi ; Bacteria ; Artwork ; Antimicrobial protection ; Biocides ; Microbiology (non-medical) ; Cultural studies ; Social & cultural history ; Ecological science, the Biosphere ; Genetics (non-medical) ; Biochemistry ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBC Cultural and media studies::JBCC Cultural studies ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of comparative physiology 178 (1996), S. 329-336 
    ISSN: 1432-1351
    Keywords: Grasshopper ; Sexual behavior ; Spermatophore ; Accessory gland secretion ; Surgical ablations ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In the female grasshopper Gomphocerus rufus mating elicits ‘secondary defense’ which makes remating impossible. The behavioral change is caused by the liquid white secretions, proteins of less than 90 kD, which are produced by the white tubuli of the male's accessory glands. Experimental injection of the white secretions directly into the spermathecal duct of receptive virgins provokes ‘secondary defense’ instantly whereas sperm transfer had no such effect. ‘Secondary defense’ is also released by eggs entering the oviducts and excerting pressure against the oviductal walls on their way to oviposition.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Calcified tissue international 24 (1977), S. 223-229 
    ISSN: 1432-0827
    Keywords: Enamel-cementum-morphology ; Immunocytochemistry ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Summary The continuously erupting rabbit incisor tooth is normally thought of as having an enamel covered “crown” on its labial surface and a cementum covered “root” on its lingual surface. We have examined both surfaces of continuously erupting rabbit incisor teeth taken from near term embryos by a variety of means, including transmission and scanning electron microscopy, biochemical fractionation, and immunohistochemistry. In all cases, we could detect no qualitative difference in the early extracellular matrices taken from the labial and lingual surfaces of the teeth. Both matrices were shown to be composed of dentin and enamel, although the thickness and geometry of the enamel matrix on the lingual surface was somewhat different from that on the labial surface.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Archives of microbiology 135 (1983), S. 141-146 
    ISSN: 1432-072X
    Keywords: Biochemistry ; Chimiotaxonomy ; Fungus wall ; Taphrina deformans
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glucose is the main component of the cell wall of the yeast form of Taphrina deformans. On the other hand the glucosamine content is very low (less than 1%). Other sugars are mannose, galactose and rhamnose; their content depends on the age of the cultures. The protein content is less than 5% and lipids less than 2%. Most of the isolated cell wall is alkalisoluble: the insoluble fraction is less than 8% of the total wall. Three polysaccharides have been detected: an α-glucan containing mostly α(1→3) and perhaps a few α(1→4) glycosidic linkages, a β-glucan containing β(1→3) and β(1→6) linkages, and a heteropolysaccharide fraction containing mannose, galactose and rhamnose. Chitin, if present, forms no more than 2‰ of the total wall. The biochemical characteristics of the cell wall of the yeast form of T. deformans distinguish it from that of filamentous Ascomycetes and Basidiomycetes and also of most of the yeasts. It is with the Schizosaccharomyces wall that they have the most features in common.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Pharmacy world & science 11 (1989), S. 3-8 
    ISSN: 1573-739X
    Keywords: Biochemistry ; Clofazimine ; Dapsone ; Ethionamide ; Isoniazide ; Mechanism of action ; Mycobacterium leprae ; Prothionamide ; Quinolones ; Ribonucleotide reductase inhibitors ; Rifampicin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract From a pharmacochemical point of view the existing anti-leprotics as well as possible innovations in the chemotherapy of leprosy are discussed. Of the main anti-leprotics, which are used nowadays — dapsone, rifampicin, clofazimine, isoniazide, ethionamide and prothionamide — the mechanism of action, the main problems in their application and possibilities to develop improved variants are reviewed. Based on the chemistry ofMycobacterium leprae, the target systems for new anti-leprotics are identified. These systems include the cell wall, the catabolism of reactive oxygen species, the metabolisms of carbon sources, the amino acid metabolism and the uptake of iron. Two possible new lead structures from other fields, 4-quinolones and mycobacterial ribonucleotide reductase inhibitors are presented.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Pharmacy world & science 13 (1991), S. 123-126 
    ISSN: 1573-739X
    Keywords: Alkylation ; Antineoplastic agents ; Biochemistry ; Cytotoxicity ; Oxidation-reduction ; Quinones
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Quinones can be metabolized by various routes: substitution or reductive addition with nucleophilic compounds (mainly glutathione and protein thiol groups), one-electron reduction (mainly by NADPH: cytochrome P-450 reductase) and two-electron reduction (by D,T-diaphorase). During reduction semiquinone radicals and hydroquinones are formed, which can transfer electrons to molecular oxygen, resulting in the formation of reactive oxygen intermediates and back-formation of the parent quinone (redox cycling). Reaction of semiquinones and reactive oxygen intermediates with DNA and other macromolecules can lead to acute cytotoxicity and/or to mutagenicity and carcinogenicity. The enhanced DNA-alkylating properties of certain hydroquinones are exploited in the bioreductive alkylating quinones. Acute cytotoxicity of quinones appears to be related to glutathione depletion and to interaction with mitochondria and subsequent disturbance of cellular energy homoeostasis and calcium homoeostasis. These effects can to a certain extent be predicted from the electron-withdrawing and electron-donating effects of the substituents on the quinone nucleus of the molecule. Prediction of cytostatic potential remains much more complicated, because reduction of the quinones and the reactivity of the reduction products with DNA are modulated by the prevailing oxygen tension and by the prevalence of reducing enzymes in tumour cells.
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  • 10
    ISSN: 1432-0878
    Keywords: Neurosecretory tract (eel) ; Transport of hormones ; Arginine-vasotocin ; Ichthyotocin ; Biochemistry ; light microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Description / Table of Contents: Résumé Une étude pharmacologique et histologique des transformations enregistrées le long du tractus neurosécrétoire est réalisée chez l'anguille européenne après hypophysectomie totale. Les animaux, sacrifiés entre 8 jours et 150 jours après hypophysectomie, sont d'abord examinés sur le plan quantitatif en suivant le devenir de l'arginine-vasotocine et de l'istotocine dans les parties antérieure (noyau préoptique) et caudale du tractus neurosécrétoire. L'étude est ensuite effectuée sur un plan qualitatif, en suivant, pour les mêmes territoires et les mêmes périodes de temps, les transformations notées pour le neurosécrétat. Les résultats obtenus au moyen de ces deux techniques d'investigation sont comparés. 1. Sur le plan quantitatif, l'expérience montre que l'évolution de l'arginine-vasotocine est différente de celle de l'isotocine, et qu'une distinction peut être faite entre les parties antérieure et caudale du tractus neurosécrétoire. En règle générale, et particuhèrement pour le premier peptide, lorsqu'il y a chute de concentration au niveau préoptique il y a augmentation de concentration dans la partie caudale, ce qui permet de traduire le cheminement des hormones. 2. L'expérience montre également que les hormones sont toujours présentes, mais subissent des chutes de concentration très importantes. 3. Le contrôle histologique confirme les résultats précédents, et montre des variations importantes dans la quantité et la colorabilité du neurosécrétat.
    Notes: Summary A pharmacological and histological study of the transformations of the neurosecretory material observed along the neurosecretory tract of the hypophysectomized eel has been performed. The animals, sacrificed within a period of 8 to 150 days after hypophysectomy, have been first examined on a quantitative level by registrating the concentration of arginine-vasotocin and ichthyotocin in the anterior (preoptic nucleus) and caudal parts of the neurosecretory tract. The study was then transferred to a qualitative level for the same regions and post-operative times, to follow up the transformations of the neurosecretory material. The results obtained with these two approaches of investigation are compared. 1. On the quantitative level, the experiments showed that the arginine-vasotocin behaves differently if compared with ichthyotocin, and that a difference exists between the anterior and caudal parts of the neurosecretory tract. In general, a decrease of concentration in the preoptic nucleus is followed by an increase of concentration in the caudal part. This is particularly obvious in the case of the arginine-vasotocin. This result speaks in favour of the transport of hormones along the neurosecretory tract. 2. The experiment showed also that the hormones are always present, but show an important decrease in concentration. 3. The histological control confirmed the pharmacological results, showing great variations of the quantity and stainability of the neurosecretory material.
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    Parasitology research 62 (1980), S. 85-93 
    ISSN: 1432-1955
    Keywords: Biochemistry ; Nematodes ; Filariae ; Setaria cervi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The microfilariae and adults ofSetaria cervi, a filarial parasite of Indian water-buffalo (Bubalus bubalis Linn.) and of other ruminants were analysed for various biochemical constituents. Both stages of the parasite were rich in protein, carbohydrate, and lipids while nucleic acids were detectable in only small amounts. Microfilariae and adults contained 10 and 25% dry matter, 57.4 and 63.0% protein, 8.9 and 14.8% carbohydrate, and 12.8 and 9.2% lipid, respectively. Reducing sugars accounted for 52 and 67% respectively of the total carbohydrate in these two stages. Glycogen accounted for 95% of total carbohydrate in the cold PCA soluble fraction of adult worms while its concentration in microfilariae was very low. Glucose was the main constitutent of reducing sugars while concentrations of fructose were very low. Microfilariae contained more lipids, nucleic acids, mucopolysaccharides, and total phosphorus than adults. The phospholipid percentage was higher in microfilariae than in adults. The amino acid pattern of both stages was very similar.
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  • 12
    ISSN: 1432-0878
    Keywords: Colchicine ; Human enterocyte ; Glycoprotein transport ; Autoradiography ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The effect of colchicine on the intracellular transport of 3H-fucose-labelled glycoproteins in the absorptive cells of cultured biopsy specimens of the human intestine was investigated by light- and electron-microscopical autoradiography and by biochemical methods. The results showed a decrease in the radioactivity of the cell coat on the microvilli and an increase in the Golgi apparatus and in the apical vesicles and tubules. This divergence is attributed to a colchicine-induced impairment of the normal transport of cell-coat glycoproteins from the Golgi apparatus, via the apical vesicles and tubules, to the apex of the cell. The radioactivity of the lysosome-like bodies in the absorptive cells cultured with colchicine also increased. This finding supports a crinophagic function of these organelles in the degradation of excess cell-coat material. The investigations were supported in part by the Foundation for Medical Research (FUNGO), which is subsidized by the Netherlands Organisation for the Advancement of Pure Research
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  • 13
    ISSN: 1075-2617
    Keywords: FMDV ; structure ; NMR spectrocopy ; NEO constraints ; RGD (Arg-Gly-Asp) ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution structure of a 20 amino acid long peptide corresponding to the region 141-160 of the envelope protein Vp1 from foot-and-mouth disease virus (FMDV) serotype A, variant A, has been determined by a combination of NMR experiments and computer calculations. The peptide contains both the immunodominant epitope as well as the sequence (RGD) used by the virus to bind the cell receptor in the initial stages of infection. These two sites have been shown to partially overlap.One hundred and thirty-five NMR distance constraints were used to obtain a set of 11 structures by distance geometry, minimization and molecular dynamics simulations. These structures were divided into two homogeneous families based upon backbone superimposition. The first and most populated family was characterized by a backbone RMS of 1.5±0.4 Å, the second by a backbone RMS of 0.8±0.2 Å. The two families had similar structural features and differed mainly in the backbone angles of G149. In the larger of the two families these angles favoured the formation of a loop comprising residues 147 to 152 and stabilized by a H-bond between the NH of D147 and the CO of A152. In the second family, where this bond was absent, the peptide adopted in this region the shape of an irregular helix. The C-terminal half of the peptide (152-159) was similar in both families and largely helical. Similar structural features were also found within the VRGDS sequence (144-148) which was assigned to a β-turn type IV. The features of the two families of structures were found to be different from those of the recently published X-ray structure of the antigenic loop of a chemically modified form of FMDV. Proposals accounting for these differences are provided which take into account the dual activity of the 141-160 sequence (i.e. antibody binding and cell invasion through receptor binding).
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  • 14
    ISSN: 1075-2617
    Keywords: FMDV ; NMR spectrocopy ; RGD (Arg-Gly-Asp) ; NEO constraints ; structure-activity correlation ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution structure of a peptide corresponding to the VP1 region 141-160 of foot-and-mouth disease virus (FMDV) serotype A variant USA has been studied by NMR and computer calculations and compared with the results from a study on a highly homologous peptide deriving from serotype A, variant A. The two peptides differ in their serological behaviour and contain the immunodominant epitope of the virus which partly overlaps with its receptor binding region. Distance constraints, derived both from 2D and 3D homonuclear NMR and 2D-heteronuclear NMR experiments, were combined with DG calculations to yield 50 structures. After refinement through EM and restrained molecular dynamics simulations the selected structures shared several general features. In particular the 151-158 region was a helix in all cases while a large loop similar to that found in peptide A but comprising less residues and stabilized by an H-bond between the side chains of D147 and S150 was found in the majority of structures. A further loop, common to all structures, was identified around the RGD sequence (145-147). This was different from that found in the corresponding region of peptide A as were the conformations of the individual residues within the RGDX sequence.The different structural features shown by the two peptides were rationalized in terms of the S148 (peptide A) to F148 (peptide USA) mutation. The second mutation, that at position 153 (L in A, P in USA) did not appear to affect the structure of the peptide significantly although the different dimensions of the loop in the central region and the type of H-bond stabilizing it could be potentially ascribed to this second mutation.All criteria used pointed to different structural features for the two peptides consistent with their serological behaviour.
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 125-133 
    ISSN: 1075-2617
    Keywords: SPPS ; labelled peptides ; cellular localization ; amphipathic peptide ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the solid-phase synthesis by the Fmoc strategy of a peptide containing a cysteamide group at its C-terminus. This peptide was subject to further modifications including the linkage of fluorophores, namely lucifer yellow and coumarin respectively, at the C- and/or N-terminals. After incubation with living cultured cells these two probes were localized and it is concluded that the post-synthesis modifications can strongly modify the localization of the peptide.
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  • 16
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 17
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 106-116 
    ISSN: 1075-2617
    Keywords: all parallel helix assemblies ; helix transition ; 310-/Α-HELICES ; two conformers ; water associated with non-polar helices ; X-ray crystallography ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The role of end groups in determining stereochemistry and packing in hydrophobic helical peptides has been investigated using an α-aminosobutyric acid (Aib) containing model nonapeptide sequence. In contrast to the Boc-analogue, Ac-(Aib-Val-Ala-Leu)2-Aib-OMe crystallizes with two independent molecules in a triclinic cell. The cell parameters are: space group P1, a=10.100(2)Å, b=15.194(4) Å, c=19.948(5) Å, α=63.12(2)°, β=88.03(2)°, γ=88.61(2)°, Z=2, R=7.96% for 5140 data where |Fo|〉3σ(F). The two independent molecules alternate in infinite columns formed by head-to-tail hydrogen bonding. The helices in the two independent molecules are quite similar to each other but one molecule is rotated ≍123° about its helix axis with respect to the other. All the helical columns pack parallel to each other in the crystal. Replacement of the bulky Boc group does not lead to any major changes in conformation. Packing characteristics are also similar to those observed for similar helical peptides.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 117-124 
    ISSN: 1075-2617
    Keywords: peptides ; neuropeptide ; antimicrobial agent ; skin secretion ; frogs ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The granular dorsal glands of the giant tree frog Litoria infrafrenata contain five peptides including caerulein (a known neuropeptide), and four new peptides named frenatins 1 (MH+ = 1140 Da), 2 (1423), 3 (2180) and 4 (2493). The amino acid sequences of the frenatins are detailed: their structures do not correspond to those of peptides isolated from other amphibians or animals. Frenatin 3, Gly-Leu-Met-Ser-Val-Leu-Gly-His-Ala-Val-Gly-Asn-Val-Leu-Gly- Gly-Leu-Phe-Lys-Pro-Lys-Ser-(OH), has wide spectrum antimicrobial properties.
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  • 19
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 141-156 
    ISSN: 1075-2617
    Keywords: gramacidin A ; channel forming peptides ; Peptide conformational analysis ; cicular dichroism ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relation between the various spatial structures of the gramicidin A channels and their ionic conductance has been studied. For this aim, various conformations of the peptide were pre-formed in liposomal bilayer and after subsequent fusion of liposomes with planar lipid bilayer the measured channel conductance was correlated with gramicidin structures established in liposomes. To form the single-stranded π6.3π 6.3 helix the peptide and lipid were co-dissolved in TFE prior to liposome preparation. THF and other solvents were used to form parallel (↑ ↑ π π) and antiparallel (↑ ↓ π π) double helices. Conformation of gramicidin in liposomes made by various phosphatidylcholines was monitored by CD spectroscopy, and computer analysis of the spectra obtained was performed. After fusion of gramicidin containing liposomes with planar bilayer membranes from asolectin, the histograms of single-channel conductance were obtained. The histograms had one or three distinct peaks depending on the liposome preparation. Assignment of the structure of the channel to conductance levels was made by correlation of CD data with conductance histograms. The channel-forming analogue, des(Trp-Leu)2-gramicidin A, has been studied by the same protocol. The channel conductances of gramicidin A and the shortened analogue increase in the following order: ↑ ↓ π π 2 ↑ ↑ π π 〈 π 6.3π6.3. Single-channels formed by double helices have higher dispersity of conductance than the π6.3π6.3 helical channel. Lifetimes of the double helical and the π6.3π6.3 helical channels are very close to each other. The data obtained were compared with theoretically predicted properties of double helices [1].
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  • 20
    ISSN: 1075-2617
    Keywords: HIV ; peptide library ; immune response ; cytokines ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hypervariable domain of the HIV gp120, the V3 loop domain, represents a target for neutralizing antibodies and for HIV vaccine strategies. In this study, we have investigated in murine species the potential cross-reactivity of immune responses elicited by immunization either with individual V3 peptides, derived from distinct HIV sequences (BRU, RF, SF2, MN and ELI sequences), or with a V3 combinatorial peptide library.We observed that individual V3 peptides are immunogenic but elicit a specific B- and T-cell immune response that is mainly restricted to the sequence of the immunizing peptide. In particular, T-cell responses that depend on T-cell receptor recognition of peptides bound to the molecules encoded by the major histocompatibility complex were significantly influenced by small differences in the peptide amino acid sequence. The combinatorial V3 peptide library, previously described as B- and T-cell immunogens, induced a more broadly reactive immune response, specially when T-cell cytokine secretion was used as a readout for restimulation of T-cells with individual V3 peptides.These data suggest that amino acid variations in the sequence of an antigenic peptide could lead to the induction of different transducing signals in the primed T-cell population and to the activation of T-cells with distinct cytokine secretion properties. These observations may have implications in the understanding of antigenic variability and in the design of vaccine strategies.
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  • 21
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    Journal of Peptide Science 2 (1996), S. 157-164 
    ISSN: 1075-2617
    Keywords: sideropore ; peusdobactin ; peusdomycin ; solution-phase peptide synthesis ; unusual amino acids ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pseudobactin is a structurally complex and physiologically important siderophore (microbial iron chelator) from Pseudomonas putida- fluorescens. Various fragments of the unusual peptide component of pseudobactin listed below were prepared by solution-phase peptide synthesis.L-Lys· D-threo-β-OH Asp· L-Ala· D-allo-Thr· L-AlaL-Lys· D-threo-βOH Asp· L-Ala· D-allo-ThrD-threo-β-OH Asp· L-Ala· D- allo-Thr· L-Ala· D-N-OH-cycloOrnD-threo-β-OH-Asp· L-Ala· D-allo-Thr· L-AlaL-Ala· D-allo-Thr· L- Ala· D-N-OH-cycloOrnA class of related peptides named pseudomycins have shown promising antifungal activity. To examine if these peptide fragments above would elicit similar activity, the fragments were tested and found to have no antifungal activity in limited bioassays.
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  • 22
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 23
    ISSN: 1075-2617
    Keywords: Nformylmethionyl peptides ; human neutrophils ; chemotaxis ; superoxide anion generation ; lysozyme release ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formylpeptides formyl-methionyl-Nmethylleucyl- phenylaline methyl ester [for-Met-(NMe)Leu-Phe-OMe] 1, formyl-methionyl-2-aminotetralin-2-carboxyl-phenylalanine methyl ester [for-Met Act-Phe-OMe] 2, formyl-methionyl-1,2,3,4-terahydroisoquinoline-3-carboxl- phenylalanine methyl ester [for-Met-Tic-Phe-OMe] 3 and formyl- methionyl-2-aminoxy-4-methylvaleryl-phenylalanine methyl ester [for-Met-OLeu-Phe-OMe] 4 were synthesized in order to investigate the role of the amide bond at position 2 on biological activities on human neutrophils. Only analogue 2, which keeps the NH group at position 2, was found to retain activity though sterically encumbered.
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  • 24
    ISSN: 1075-2617
    Keywords: NPY ; conformational analysis (CD, NMR) ; molecular dynamics ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Neuropeptide Y (NPY), a peptide amide comprising 36 residue has been shown to act as a potent vasoconstrictor. In order to shed light on the structural requirements for the biological activities with respect to the different prerequisites for affinity to the NPY receptor subtypes Y1 and Y2, in the present study the syntheses and conformational analyses of two C-terminal segments, NPY(18-36) and NPY(13-36), are described.The results obtained by CD measurements, two-dimensional NMR spectros copy and a conformational refinement of the NMR-derived structure by molecular mechanics simulations support the findings of previously published structure -activity relationship studies for biologically active and selective compounds. In particular, the α-helical conformation as well as an appropriate exposure of the side chains of the critical C-terminal dipeptide within NPY(18-36) are in agreement with the prerequisites proposed for Y2 receptor binding of that segment.
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  • 25
    ISSN: 1075-2617
    Keywords: antimicrobial peptides ; hydrophobic residue ; ion-channels ; pores ; α-helix ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The design of cecropin-melittin hybrid analogues is of interest due to the similarities in the structure of the antimicrobial peptides cecropin and melittin but differences in their lytic properties. We suspected that a hydrophobic residue in position 2 of milittin (Ile8 in the hybrid) plays an important role in the activity of the 15-residue hybrid, KWKLFKKIGAVLKVL-NH2, [CA(1-7)M(2-9)NH2] and have now examined its role in the analogue toward five test bacteria. Deletion of Ile8 reduced activity, and it was not restored by lengthening to 15 residues by addition of another threonine at the C-terminus. Replacement of Ile8 by a hydrophobic leucine maintained good activity and Ala8 was equally active for four organisms, although less active against Staphylococcus aureus. Replacement by the hydrophilic Ser8 strongly reduced potency against all five organisms. Deletion of Leu15 decreased activity, but addition of Thr16 maintained good activity. The presence of hydrophobic residues appears to have a significant effect on the process of antibacterial activity. These peptide analogues showed voltage-dependent conductance changes and are capable of forming ion-pores in planar lipid bilayers. The antibacterial action of the peptides is thought to be first an ionic interaction with the anionic phosphate groups of the membrane followed by interaction with the hydrocarbon core of the membrane and subsequent reorientation into amphipathic α-helical peptides that form pores (ion-channels), which span the membrane. The analogue also showed an increase in α-helicity with an increase in hexafluoro 2-propanol concentration.
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  • 26
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    Journal of Peptide Science 2 (1996), S. 233-239 
    ISSN: 1075-2617
    Keywords: NMR ; chemical shift estimation ; restrained refinement ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For flexible peptides, nuclear Overhauser Effects (NOE) experiments do not provide enough information to ensure a correct definition of their solution structure. The use of distance constraints, derived from the knowledge of proton chemical shifts, is developed to restrict the number of possible conformations. In the case of flexible molecules, randomization appears as an important factor of the correct estimation of the chemical shifts from the 3D structure. The refinement of the solution structure of the highly flexible AVP-like parallel dimer is described to illustrate this process.
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  • 27
    ISSN: 1075-2617
    Keywords: mucin glycopeptides ; tumour associated antigen ; cancer ; MHC Class II binding ; glycopeptide synthesis ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of peptides and glycopeptides derived by amino acid and glycosyl amino acid scans through the self peptide from CBA/J mouse haemoglobin Hb (67-76), VITAFNEGLK, was synthesized by multiple column peptide synthesis (MCPS). Investigation of glycopeptide binding to the mouse major histocompatibility class II molecule Ek showed that glycans in position 72 did not interfere with the binding to Ek. Immunization experiments revealed that glycopeptides with the glycan in position 72 were immunogenic. Therefore a series of N-linked and O-linked glycopeptides with the glycan attached in the position 72 either to serine, threonine or asparagine was synthesized by MCPS. The glycan structure was furthermore varied with respect to monosacc haride component, size of oligosaccharide, anomer configuration and stereoche mistry of essential hydroxyl groups in order to investigate the specificity of the interaction with the T-cell receptor. Easy synthesis of ready to use Ser and Thr building blocks corresponding to mucin core 1, the Tn-antigen and its β-anomer were developed using trichloroacetimidates as glycosyl donors and reduction with in situ acetylation of the azide containing glycosylation products. Synthesis of an α-linked GlcNAc-Thr building block was achieved by glycosylation of Fmoc-Thr-OPfp with 2-azido-2-deoxy-3,4,6-tri-O-acetyl-D- glycopyranosyl trichloroacetimidate as a glycosyl donor. Other building blocks were obtained by previously described procedures.
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  • 28
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    Journal of Peptide Science 2 (1996), S. 195-211 
    ISSN: 1075-2617
    Keywords: peptide absorption ; dipeptide carrier ; brush border membrane ; M-cell, Caco-2 cell ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Today there is considerable interest in oral peptide delivery. However, oral administration of peptides is limited by a low bioavailability and a high variability in plasma levels. A review is given of the literature describing the major barriers in peptide absorption, the basic mechanisms of intestinal peptide transport, the experimental models and the pharmaceutical approaches currently used in the investigation of peptide and protein absorption processes.
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  • 29
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    Journal of Peptide Science 2 (1996), S. 252-260 
    ISSN: 1075-2617
    Keywords: melittin immunogenicity ; antigen recognition ; membrane involvement ; haptenic position ; late IgG responses ; cellular dynamics ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Melittin peptides carrying 2,4-dinitro-6-carboxyphenyl (Dncp) haptenic groups regularly evoked anti-hapten IgG responses in mice or guinea pigs when the hapten was C-terminally attached. Single haptens on the N-terminal helix in several positions gave poor or no responses in the early stages but adequate titres after prolonged immunization. Peptides with Dncp at the C-terminus as an invariant feature and a second Dncp in various positions along the peptide chain did not fail to produce adequate responses. The hampering effect is not due to a defect at the T-cell level but involves the recognition step on the B-cell. It is implied that the haptenic interaction with the paratope of the recognizing immunoglob ulin on the B-cell involves the cell membrane in an important way. It is also suggested that late antibody responses should not be overlooked during the development of proteinaceous immunogens for vaccination.
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  • 30
    ISSN: 1075-2617
    Keywords: substance P ; agonist ; conformational constraint ; backbone cyclization ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Novel backbone-to-side chain and backbone-to-backbone cyclic analogues of substance P (SP) were prepared by solid-phase synthesis and screened for biological activity. An analogue containing a thioether- lactam ring between positions 9 and 11 showed an EC50 value of 20nM toward the neurokinin 1 (NK-1) and was inactive toward the NK-2 and NK-3 receptors. On the other hand, in a multiple backbone cyclic peptide library of similar analogues, in which the sulphur was excluded from the ring, very low activity was detected. The activity was re-evaluated and was found to be even lower (EC50=0.11 mM) than the previously published data. These results indicate that the thioether moiety has a crucial role in receptor activation. The results also show tolerance of the NK-1 receptor, but not NK-2 or NK-3, to cyclization of the C-terminal portion of the SP6-11 hexapeptide.
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  • 31
    ISSN: 1075-2617
    Keywords: opioid peptides ; selectivity ; antagonism ; conformation ; NMR ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The sequence of deltorphin I, a δ-selective opioid agonist, has been systematically modified by inserting conformationally constrained Cα,α disubstituted apolar residues in the third position. As expected, substitution of Phe with Ac6c, Ac5c and Ac3c yields analogues with decreasing but sizeable affinity. Surprisingly, substitution with Aib yields an analogue with almost the same binding affinity of the parent compound but with a greatly increased selectivity. This is the first case of a potent and very selective opioid peptide containing a single aromatic residue in the message domain, that is, only Tyr1. Here we report a detailed conformational analysis of [Aib3]deltorphin I and [Ac6c3]deltorphin I in DMSO at room temperature and in a DMSO/water cryomixture at low temperature, based on NMR spectroscopy and energy calculations. The peptides are highly structured in both solvents, as indicated by the exceptional finding of a nearly zero temperature coefficient of Val5 NH resonance. NMR data cannot be explained on the basis of a single structure but it was possible to interpret all NMR data on the basis of a few structural families. The conformational averaging was analysed by means of an original computer program that yields qualitative and quantitative composition of the mixture. Comparison of the preferred solution conformations with two rigid δ-selective agonists shows that the shapes of [Aib3]deltorphin I and [Ac6c3]deltorphin I are consistent with those of rigid agonists and that the message domain of opioid peptides can be defined only in conformational terms.
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  • 32
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    Journal of Peptide Science 2 (1996), S. 318-324 
    ISSN: 1075-2617
    Keywords: p53 protein ; peptide immunomodulators ; TP5 analogues ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Taking into account the sequence homology existing between thymopoietin II and the DNA-binding domain of p53 protein, a series of octapeptides was synthesized, related to the wild p53 type protein as well as to its mutated forms, appearing in some human tumours. The wild type octapeptide has immunostimulative activity with regard to the humoral immune response, but is inactive in the cellular immune response. The mutated peptides of p53 differ in their immunomodulatory activity from the wild type octapeptide. The Ser5 analogue of the wild type peptide is a strong stimulant of the humoral immune response and enhances TNF-α production, while at the same time suppressing the cellular immune response. The data suggest that the mutations of p53, which favour tumour development and growth, may also change the immune activity of respective p53 fragments.
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  • 33
    ISSN: 1075-2617
    Keywords: conformational constraints ; CD spectroscopy ; fluorescence quenching ; synthetic peptides ; tyrosine phosphorylation ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We synthesized by classical solution methods three conformational constrained analogues of EDNEYTA, a heptapeptide sequence that represents the common major autophosphorylation site of the protein tyrosine kinases (PTKs) of the Src family. The correlation between the different structural properties induced by the modifications of the native sequence and the propensity of the peptides to act as PTK substrates was examined. The kinetic data obtained indicate that the introduction of the tyrosine-analogue constraints Tic(OH) and MeTyr, which block the ring flexibility, completely prevents the phosphorylation catalysed by the kinases Lyn and Fgr. On the other hand PTKIIB/p38syk can phosphorylate the two derivatives albeit with an efficiency lower than that found with the native sequence. A third derivative contained side chain to side chain cyclization. This analogue, in which the freedom of the phenolic moiety is not altered, can be phosphorylated by all the PTKs tested with kinetic constants comparable to the parent peptide.
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  • 34
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 35
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    Journal of Peptide Science 2 (1996), S. 351-356 
    ISSN: 1075-2617
    Keywords: DPDPE ; enkephalins ; NMR structure analysis ; molecular dynamics simulations ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of [D-Pen2,D-Pen5] enkephalin (DPDPE), a highly potent δ-selective opioid agonist, was examined by means of NMR, molecular mechanics and molecular dynamics methods. The structural information in the solvent water was obtained employing one- and two-dimensional methods of 1H and 13C-NMR spectroscopy. Based on the distance geometry technique using the ROE data as input, 400 conformers were obtained and considered in the structure analysis. Alternatively, about 2000 conformers were stochastically generated and related to the NMR data after energy minimization. The structure analysis provides one conformer in agreement with all NMR data, which belongs to the lowest energy conformation group. This structure may serve as a reference conformer for DPDPE analogues synthesized with the aim of activity increase.
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  • 36
    ISSN: 1075-2617
    Keywords: Biosynthesis ; deuterium ; nitrogen 15 ; positive ion FAB mass spectrometry ; ion channel-forming peptide ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple procedure for the preparation of the specifically labelled peptide antibiotic zervamicins IC, IIA and IIB has been developed. The zervamicin molecules are labelled with stable isotopes by culturing the Emericellopsis salmosynnemata on a well-defined synthetic medium containing the highly isotopically enriched amino acid. To obtain the peptide with the specifically and highly enriched amino acid residue, precautions have been taken to prevent any de novo biosynthesis of the particular amino acid from unlabelled precursors. The enrichment of the labelled peptide is determined by mass spectrometric analysis. Following this method we have incorporated [2′,4′, 5′,6′,7′-2H5]-L-Trp-1, [1′-15N]-L-Trp-1 and [2′, 3′,4′,5′,6′-2H5]-L- Phl-16 into zervamicins IC, IIA and IIB on the preparative scale and without scrambling of the label. Thus, using the procedures described, isotopically labelled zervamicins can be prepared, allowing them to be studied by solid- state NMR.
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  • 37
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    Journal of Peptide Science 2 (1996), S. 364-370 
    ISSN: 1075-2617
    Keywords: conformation ; glutamine ; folding ; simulation ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational preferences of the methylenic sequence in the side chain of the glutamine residue were investigated by ab initio and semi-empirical quantum mechanical calculations and examination of both the Brookhaven Protein Databank and Cambridge Structural Data Base. The results were analysed on the basis of our previous findings about the folding of methylene groups in aliphatic segments. Both energy calculations and the crystallographic structure of small peptides indicate that methylene units of the glutamine residue tend to fold in a gauche conformation. In contrast, such groups usually adopt an all-trans conformation in proteins due basically to the entropic and solvent contributions. These results have been demonstrated by computing the entropic correction to the free energy and evaluating the solvent effects through SCRF calculations
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  • 38
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 39
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    Journal of Peptide Science 2 (1996), S. 381-391 
    ISSN: 1075-2617
    Keywords: conformational analysis ; crystal structure ; folded structures ; pseudopeptides ; reduced peptides ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reduced dipeptides with the general formula RCO-Xaa- rXbb-N+HR′R′′ (rXbb, reduced analogue of residue Xbb: NH-Cα HR1 -Cr H2) are shown to adopt a folded conformation in solution and in the solid state. The protonated reduced amide bond is an active proton donor capable of interacting with a peptide carbonyl to give a strong hydrogen bond topologically equivalent to the i+2 or i+3⇒ i interaction. The resulting conformation is similar to the γ- or β-turn structure found in peptides and proteins.
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  • 40
    ISSN: 1075-2617
    Keywords: β-turns ; folded conformation ; dehydro-residue ; X-ray diffraction ; consecutive dehydro-residue ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To obtain general rules of peptide design using α,β-dehydro-residues, a sequence with two consecutive ΔPhe-residues, Boc-L-Val-ΔPhe-ΔPhe- L-Ala-OCH3, was synthesized by azlactone method in solution phase. The peptide was crystallized from its solution in an acetone/water mixture (70:30) in space group P61 with a=b=14.912(3)  Å, c= 25.548(5)  Å, V=4912.0(6)  Å3. The structure was determined by direct methods and refined by a full matrix least-squares procedure to an R value of 0.079 for 2891 observed [I≥3σ(I)] reflections. The backbone torsion angles φ1=-54(1)°, ψ1= 129(1)°, ω1=-177(1)°, φ2 =57(1)°, ψ2=15(1)°, ω2 =-170(1)°, φ3=80(1)°, ψ3 =7(2)°, ω3=-177(1)°, φ4 =-108(1)° and ψT4=-34 (1)° suggest that the peptide adopts a folded conformation with two overlapping β-turns of types II and III′. These turns are stabilized by two intramolecular hydrogen bonds between the CO of the Boc group and the NH of ΔPhe3 and the CO of Val1 and the NH of Ala4. The torsion angles of ΔPhe2 and ΔPhe3 side chains are similar and indicate that the two ΔPhe residues are essentially planar. The folded molecules form head-to- tail intermolecular hydrogen bonds giving rise to continuous helical columns which run parallel to the c-axis. This structure established the formation of two β-turns of types II and III′ respectively for sequences containing two consecutive ΔPhe residues at (i+2) and (i+3) positions with a branched β-carbon residue at one end of the tetrapeptide.
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  • 41
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    Journal of Peptide Science 2 (1996), S. 245-251 
    ISSN: 1075-2617
    Keywords: enkephalin ; neurotensin ; opioid receptor affinity ; multivalent ligand ; liposome ; fluorescence microscopy ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A multivalent ligand system was constructed by coimmobilization of two kinds of peptide ligands, enkephalin and neurotensin derivatives having a dioctadecyl group, on dimyristoylphosphatidylcholine (DMPC) liposomes. The enkephalin derivatives are Tyr-D-Ala-Gly-Trp-Leu- (Sar-Sar-Pro)n-[N(C18H37)2] (Enk3nD, n=0, 1, 2), where a dioctadecyl group was connected to the C-terminal side of enkephalin directly or through a hydrophilic and flexible spacer chain of different lengths. The neurotensin derivatives are Ac-Glu[N(C18H37)2]-(Sar-Sar-Pro)n-Arg-Arg-Pro-Tyr-Ile-Leu-OH (D3nNT, n=0, 1, 2, 3). The derivatives were spontaneously immobilized on DMPC liposomes by overnight incubation. The receptor affinity of the enkephalin derivatives became significantly higher upon immobilization on liposomes. The highest affinity was obtained for the δ receptor by Enk6D immobilized on DMPC liposomes. This affinity is higher than that of enkephalinamide. Neurotensin derivatives coimmobilized with large amounts of Enk3D on DMPC liposomes show higher affinity than the neurotensin derivatives immobilized alone. The effect of Enk3D on the receptor affinity of the coimmobilized neurotensin derivative disappeared by the addition of [Ala2, MePhe4, Gly-ol5]enkephalin (DAGO). Therefore, the receptor affinity of a peptide hormone is altered by immobilization on DMPC liposomes and by coimmobilization with other peptide hormones. It was confirmed by fluorescent microscopy that the multivalent ligand system binds to receptors without release of the bound ligands from DMPC liposomes.
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  • 42
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    Journal of Peptide Science 2 (1996) 
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    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 43
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    Journal of Peptide Science 2 (1996), S. 271-275 
    ISSN: 1075-2617
    Keywords: peptide synthesis ; cysteine ; racemization ; enantiomeric resolution ; capillary electrophoresis ; gas chromatography ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method has been developed for the rapid determination of D-cysteine contents in synthetic peptides. It is based on the reduction of cystine residues, when present, with tris- alkylphosphines, selective derivatization of the cysteine residues with 4-vinylpyridine, followed by acid hydrolysis of the (4-pyridylethyl)cysteine -peptides. Baseline enantiomeric resolution of theD,L-S-β-(4-pyridylethyl)cysteine, and thus quantification ofD- enantiomer contents at levels ≤1%, is easily achieved by capillary zone electrophoresis exploiting the host-guest complexation principle with crown ethers or by gas chromatography on chiral glass capillary columns upon conventional derivatization of the hydrolysate. The acid-stability of the (4-pyridylethyl)cysteine derivative prevents racemization via thiazoline intermediates and allows for standardization of the acid hydrolysis-dependent racemization.
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  • 44
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    Journal of Peptide Science 2 (1996), S. 240-244 
    ISSN: 1075-2617
    Keywords: solid-phase synthesis ; peptide synthesis ; multiple synthesis ; inclusion volume synthesis ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solid-phase synthesis of peptides was carried out using only the volume of the solvent included in the swollen solid-phase resin beads [inclusion volume synthesis]. This approach enables (i) the use of higher concentrations of activated amino acids, resulting in increased coupling rates, (ii) drastically decreased consumption of solvents, and (iii) the construction of multiple peptide synthesizers having virtually no reaction vessels.
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  • 45
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    Journal of Peptide Science 2 (1996), S. 309-317 
    ISSN: 1075-2617
    Keywords: solid-phase synthesis ; calcium channel blocker ; spider toxins ; side reaction ; peptide folding ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ω-Agatoxin IVA, isolated from the venom of funnel web spider Agelenopsis aperta, blocks potently and selectively P-type calcium channels. This toxin, composed of 48 amino acids and containing 8 cysteine residues, was synthesized by the solid-phase procedure. The Cys residues were protected by acetamidomethyl (Acm) groups which were removed by mercuric acetate. During treatment with mercuric acetate, a by-product was detected, involving modification of tryptophan residues by the Acm groups. This side reaction can be completely prevented by addition of an excess of tryptophan in the reaction medium during Acm deprotection.The resulting peptide was submitted to an oxidative refolding, in different conditions, in order to determine the most favourable protocol. After formation of the four disulphide bonds, the toxin was purified by successive preparative HPLC, on two different supports, and fully characterized by analytical HPLC, capillary electrophoresis, amino acid analysis, mass spectrometry and Edman degradation. It was found to block the P-type calcium channel with a similar biological potency as described for the natural product.
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  • 46
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    Journal of Peptide Science 2 (1996), S. 279-289 
    ISSN: 1075-2617
    Keywords: peptide synthesis ; frozen aqueous solution ; protease ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: During the past decade proteases have been widely used as catalysts in peptide synthesis. Unfortunately, they are not ideal ligases. Enzymatic peptide synthesis in frozen aqueous systems has been developed as an approach towards the suppression of competitive reactions. This paper summarizes reports concerning the behaviour of non-enzymatic as well as of enzyme-catalysed reactions when the reaction mixture is frozen. The advantages of freezing the reaction mixture in serine and cysteine protease-catalysed peptide synthesis, the influence of modified reaction conditions and the possible reasons for the yield-increasing effect of freezing are discussed.
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  • 47
    ISSN: 1075-2617
    Keywords: β-bend ; cyclic amino acid ; 310-helix ; peptide conformation ; X-ray diffraction ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete series of terminally blocked, monodispersed homo-oligopeptides (to the pentamer level) from the sterically demanding, medium-ring alicyclic Cα,α-disubstituted glycine 1-aminocyclooctane-1-carb oxylic acid (Ac8c), and two Ala/Ac8c tripeptides, were synthesized by solution methods and fully characterized. The preferred conformation of all the oligopeptides was determined in deuterochloroform solution by IR absorption and 1H-NMR. The molecular structures of the amino acid derivative Z-Ac8c-OH, the dipeptide pBrBz- (Ac8c)2-OH and the tripeptide pBrBz-(Ac8c)3-OtBu were assessed in the crystal state by X-ray diffraction. Conformational energy computations were performed on the monopeptide Ac-Ac8c-NHMe. Taken together, the results obtained strongly support the view that the Ac8c residue is an effective β-turn and helix former. A comparison is also made with the conformational preferences of α-aminoisobutyric acid, the prototype of Cα, α-disubstituted glycines, and of the other members of the family of 1-aminocycloalkane-1-carboxylic acids (Acnc, with n=3, 5-7) investigated so far. The implications for the use of the Ac8c residue in peptide conformational design are considered.
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  • 48
    ISSN: 1075-2617
    Keywords: Structure of amatoxin analogues ; constrained bicyclopeptides ; NMR ; molecular dynamics ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The evaluation of peptide structures in solution is made feasible by the combined use of two-dimensional NMR in the laboratory (NOESY) and rotating frames (ROESY), and by the use of molecular dynamics calculations. The present paper describes how both the NMR method and molecular dynamics calculations were applied to very rigid synthetic bicyclic peptides that are analogues of natural amatoxins. The NMR theory, which allows the estimate of interatomic distances between interacting nuclei, is briefly discussed. The experimental data were compared with those of known solid-state structures. Three amatoxin analogues have been examined. Of these, one is biologically active (S-deoxo γ[R] OH-Ile3-amaninamide) and its structure in the solid state has recently been worked out. The second and third analogues (S-deoxo-Ile3 -Ala5-amaninamide and S-deoxo-D-Ile3 -amaninamide, respectively) are inactive and their solid-state structures are unknown. The data presented confirm the authors' previous hypothesis that lack of biological activity of S-deoxo-Ile3-Ala5- amaninamide is due to the masking of the tryptophan ring by the methyl group of L-Ala and not to massive conformational changes of the analogue.
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  • 49
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    Journal of Peptide Science 2 (1996), S. 40-46 
    ISSN: 1075-2617
    Keywords: Tetrabenzo[a,c,g,i]fluorenyl-17-methoxycarbonyl ; Tbfmoc ; peptide synthesis ; solid-phase synthesis ; MCP-1 ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The affinity-based Nα-amino protecting group tetrabenzo [a,c,g,i]fluorenyl-17-methoxycarbonyl (Tbfmoc) has been utilized as a hydrophobic probe to allow the simple, quick and highly effective isolation of a 76 residue cysteine-containing protein (MCP-1). The base-labile Tbfmoc group can be removed under very mild conditions, which preserve the thiol-con taining protein in the reduced state. Oxidative folding was then used to furnish the biologically active β-chemokine MCP-1.
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  • 50
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    Journal of Peptide Science 2 (1996), S. 59-65 
    ISSN: 1075-2617
    Keywords: Aminoisobutyric acid ; glycine ; cyclic peptides ; X-ray diffraction ; β-turns ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have synthesized and crystallized the cyclic peptide (Gly-Aib-Gly) 2. Its structure has been determined by conventional X-ray diffracti on methods. In the crystal it adopts a conformation with one β-turn (type I) and its mirror image at the other side of the ring. All conformation al angles are similar to those reported for these amino acid residues. In particular the Aib residue has a conformation intermediate between α- and 310-helical conformations. The ring is an adequate model for the β-turn conformation. A molecule of formic acid is found in the crystal which shows a very short hydrogen bond with one of the glycine carbonyl groups.
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  • 51
    ISSN: 1075-2617
    Keywords: Solution synthesis ; human midkine ; powerful solvent system ; powerful solvent system ; active region ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Human midkine (hMK), a novel heparin-binding neurotrophic factor consisting of 121 amino acid residues with five intramolecular disulphide bonds, was synthesized by solution procedure in order to demonstrate the usefulness of our newly developed solvent system, a mixture of dichloromethane or chloroform and trifluoroethanol. The final protected 121-residue peptide was assembled from two large fully protected intermediates, Boc-(1-5 9)-OH and H-(60-121)-OBzl, in CHL/TFE (3:1, v/v) using water-soluble carbodiimide in the presence of HOOBt as coupling reagents. After removal of the protecting groups by HF followed by treatment with Hg(OAc)2 in 50% acetic acid, the fully deprotected peptide was subjected to the oxidative folding reaction. The final product was confirmed to have the correct disulphide structure from its tryptic peptide mapping and to possess the same biological activities as those of the natural product. In order to clarify the active region of the hMK molecule, the N-terminal and C-terminal half domains [(1-59) and (60-121)] were also synthesized by the same procedure used for the hMK synthesis. The C-half domain was confirmed to show the full pattern of bioactivities except for the neuronal cell survival activity, while the N-half one showed much less activity in general.
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  • 52
    ISSN: 1075-2617
    Keywords: Dehydro-peptides 310-helix ; helix reversal ; crystal structure ; circular dichroism ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The pentapeptide Boc-Val-ΔPhe-Gly-ΔPhe-Val-OMe, containing two dehydro-phenylalanine (ΔPhe) residues, has been synthesized and its structure investigated. In the crystalline state, the molecule adopts a right-handed 310-helical conformation stabilized by two intramolecular hydrogen bonds between CO of Val1 and NH of ΔPhe4, and between CO of ΔPhe2 and NH of Val5, respectively. NMR measurements are consistent with the presence of 310-helical structures also in acetonitrile and dimethylsulphoxide solution: the distances between backbone protons estimated from NOE connectivities are in overall agreement with those observed in the solid state; the chemical shifts of the amide protons show the smaller temperature coefficients for the NHs that in solid state are involved in intramolecular hydrogen bonds. The CD spectra in acetonitrile, chloroform, methanol and dimethylsulphoxide display exciton couplets of bands corresponding to the ΔPhe electronic transition at 280nm; the sign of the bands is consistent with the presence of helical structures having a prevalent left-handed screw sense. Addition of 1,1,1,3,3,3-hexafluoro- propan-2-ol gives rise to the gradual appearance of a couplet of opposite sign, suggesting the helix reversal from left-handed sense to right-handed sense. The conformational behaviour is discussed on the basis of the specific sequence of the peptide.
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  • 53
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    Journal of Peptide Science 2 (1996), S. 1-1 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 54
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 55
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    Journal of Peptide Science 2 (1996), S. 66-72 
    ISSN: 1075-2617
    Keywords: MAPS ; Pam3Cys ; polyoxime ; polypeptide vaccine ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthetic lipopeptides are showing promise as vaccine candidates, but until now it has been very difficult to prepare them in homogeneous form. We describe the synthesis and characterization of a new water-soluble, four-branched template with a built-in lipophilic adjuvant (Pam3Cys). Through the use of oxime chemistry, we attached four copies of an unprotected influenza virus peptide and characterized the product (13kDa) by reversed-phase HPLC and electrospray ionization mass spectrometry. Several other such constructions were made using the new template and different peptides. We seem to have a general method for making synthetic lipopeptides in homogeneous form.
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  • 56
    ISSN: 1075-2617
    Keywords: crown ether ; fragment condensation ; peptide synthesis ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have previously described the conditions by which peptide synthesis by the solid-phase fragment condensation approach can be carried out using crown ethers as non-covalent protection for the Nα -amino group. Here we demonstrate that the procedure can be extended to large, partially protected peptide fragments possessing free Lys and/or Arg residues. The first step was to ensure that complex formation on the side chain of amino acids was not detrimental to the methodology and exhibited the same solubility and coupling properties as Nα -complexed peptides. Thus, a model hexapeptide was synthesized using Fmoc chemistry containing Lys and Arg residues, which, when complexed with 18-Crown-6, was readily soluble in DCM and coupled quantitatively to a resin-bound tetrapeptide. Two tripeptides were then prepared, one containing a free Ser residue, the other free Tyr, to examine the possible occurrence of side reactions. After coupling using standard conditions only the former tripeptide exhibited the formation of the O-acylation by-product (5%). Another model hexapeptide containing Lys, Tyr, Ser and Asp protected with a TFA-stable adamantyl group was complexed with 18-Crown-6 and coupled to the resin-bound tetrapeptide with near quantative yield. Extending the length of the peptide to 21 and 40 residues, which represent sequences Gly52 to Leu72 (21-mer) and Pro33 to Leu72 (40-mer) from Rattus norvegicus chaperonin 10 protein, respectively, resulted in partially protected fragments that were readily soluble in water, thus enabling purification by RP-HPLC. Complexation with 18-Crown-6 gave two highly soluble products that coupled to resin-board tetramer with 68% and 50% coupling efficiencies for the 21-mer and 40-mer, respectively. Treatment with 1% DIEA solutions followed by acidolytic cleavage and purification of the major product confirmed that the correct product had been formed, when analysed by amino acid analysis and ESI-MS. These results served to extend the methodology of non-covalent protection of large partially protected peptide fragments for the stepwise fragment condensation of polypeptides.
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  • 57
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    Pharmacy world & science 14 (1992), S. 297-304 
    ISSN: 1573-739X
    Keywords: Biochemistry ; Didanosine ; Drug evaluation ; Pharmacokinetics ; Pharmacology ; Side effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract In this article the literature about didanosine, an antiretroviral drug, is reviewed. The mechanism of action, biochemical pharmacology, pharmacokinetics, and clinical results of phase-I trials are discussed. Serious adverse effects such as pancreatitis and peripheral neuropathy have occurred in these trials. An antiretroviral effect was observed in terms of an increase in CD4+ lymphocytes and a decrease in p24 antigen levels in HIV-infected individuals. Didanosine seems to be a promising drug against HIV infection, but knowledge about its clinical efficacy is scanty.
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  • 58
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    Pharmacy world & science 8 (1986), S. 209-222 
    ISSN: 1573-739X
    Keywords: Biochemistry ; Pharmacology ; Receptors, adrenergic, beta ; Review
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Developments in the receptor concept have greatly influenced our current knowledge of the beta-adrenoceptor. The triad of pharmacology, organic chemistry and studies in structure-activity relationships is discussed along historical lines, as it has been and still is an impetus for progress in the biochemistry of ligand-receptor interactions. With respect to the beta-adrenoceptor complex these advances which have led to a model in which three protein structures are functionally interacting within the frame of the cell wall: the beta-adrenoceptor, the regulatory guanine nucleotide binding protein, and the enzyme adenylate cyclase, are reviewed.
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  • 59
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    Pharmacy world & science 11 (1989), S. 146-150 
    ISSN: 1573-739X
    Keywords: Agonists ; Antagonists ; Biochemistry ; Central nervous system ; Ligands ; Pharmacology ; Receptors, histamine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The role of histamine in brain function is discussed. A brief review is presented on the three types of histamine receptors with regard to their biochemistry and functions, as well as on specific ligands, both agonists and antagonists. It is concluded that several aspects of the pharmacology of histamine in the central nervous system are still a matter of empirism and speculations. The recent publications on the brain-penetrating H2 antagonist zolantidine and the selective H3 agonists and antagonists are expected to contribute to the knowledge of the histaminergic pathways in the brain. Therapeutical areas within the central nervous system are related to behaviour (including wake-sleep), neuroendocrinal processes, the control of muscle activity and cerebral circulation.
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  • 60
    ISSN: 1432-0878
    Keywords: Key words Molecular biology ; Cell biology ; Bioassay ; Analytical chemistry ; Biochemistry ; Diagnosis ; Therapy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Significant amounts of endogenous biotin were detected by avidin-peroxidase in fixed rat kidney, liver, and brain. The staining was indistinguishable from the true signals of immunoreactivity and could not be consistently blocked by pretreatment with avidin. The finding that certain neurons in the hippocampus contain more biotin than neurons in other areas of the brain suggests that biotin might have novel functions in the brain other than its well-known role as cofactor of carboxylases. Critical examination of published immunohistochemical localization studies on rat kidney strongly suggests that many false-positive results have been considered as true signals. Interference of endogenous biotin in any study using avidin-biotin technology must be considered if biological tissues are involved. The published data obtained by this method should therefore be reevaluated. Furthermore, appropriate controls, blockers and caution in interpreting results must be exercised, not only in immunohistochemistry but also in any applications of avidin-biotin technology.
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  • 61
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    Cell & tissue research 169 (1976), S. 193-209 
    ISSN: 1432-0878
    Keywords: Planaria ; Starvation ; Fine structure ; Biochemistry ; Cytochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Employing a combination of microscopical, biochemical and autoradiographic techniques, the primary effects of starvation on adult Polycelis tenuis have been studied. Over a five week period of starvation there is on average a 32% decrease in the size of the organism. This decrease is contributed to by a reduction in mitosis and an increase in cell shrinkage autolysis and death. During starvation (following a sharp rise in RNA synthesis) there is a distinct sequence of events; four peaks of acid phosphatase activity can be resolved. The first is associated with the immediate response of the gastrodermis to feeding; the second (after 6 to 7 days) with increased autophagy and dedifferentiation in the gland cells and with muscle lysis; the third peak (after 14 to 15 days) is contributed to largely by the lysis of cells in the gut and the fourth peak (after 25 to 26 days) is caused by an extensive lysis of the reproductive system. Fine structural changes involving increased intracellular vacuolation, autophagy, crinophagy, atrophy of muscle, increased intercellular space and loss of basement membrane matrix have been related to changes in enzyme pattern. Nerve cells appear unchanged throughout the first five weeks of starvation. Pigment and gland cells loose their characteristic granules, dedifferentiate and become morphologically similar to the undifferentiated neoblasts. Dedifferentiation and the mechanisms involved in the survival of starvation are discussed.
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  • 62
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    Cell & tissue research 114 (1971), S. 365-389 
    ISSN: 1432-0878
    Keywords: Forestomach epithelium ; Goat ; ATPases ; Cytochemistry ; Ultrastructure ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Description / Table of Contents: Zusammenfassung Am Epithel der drei Vormägen der Ziege wurden licht- und elektronenmikroskopische Untersuchungen über den Nachweis der Mg++-, (Mg++-Na+-K+)- und der Ca++-aktivierbaren ATPasen durchgeführt. Bereits an lichtmikroskopischen Präparaten wurde festgestellt, daß sich deutliche Unterschiede in der Enzymaktivität der Mg++- und Ca++ stimulierbaren ATPasen sowohl für die einzelnen Epithelschichten als auch für die verschiedenen Bereiche der Vormägen nachweisen lassen; die tiefen Epithellagen reagieren stets stärker als die oberflächlichen. Ferner ist die in hohem Maße von der Inkubationszeit abhängige Reaktionsstärke im Epithel des Blättermagens größer als in der Lamina epithelialis des Netzmagens und vor allem in jener des Pansens. Bei dem elektronenmikroskopisch geführten Nachweis der ATPasen zeigt sich, daß die Reaktionsprodukte an der Außenseite der Zellmembranen liegen. Frei von Niederschlägen sind alle Zellmembranabschnitte, die sich an der Bildung der Desmosomen und Halbdesmosomen beteiligen sowie die basalen Abschnitte der Basalzellen. Im Hinblick auf die Verteilung und feinstrukturelle Lokalisation konnten keine Unterschiede zwischen den Mg++-, Ca++- und (Mg++-Na+-K+)-aktivierbaren ATPasen beobachtet werden. In Anlehnung an die Methode nach Coleman u.a. (1967) wurden Zellmembranen von Pansenepithelzellen isoliert und an diesen biochemische Enzymbestimmungen durchgeführt. Die Ausbeute der gewonnenen Zellmembranen betrug, gemessen anhand der 5′-Nukleotidase, dem Leitenzym für Plasmamembranen, gegenüber dem eingesetzten Gesamthomogenat 0,3%. Die mit diesem Verfahren durchgeführten biochemischen Enzymbestimmungen erbrachten den Nachweis, daß in den Plasmamembranen der Pansenepithelzellen neben der Mg++- und Ca++-aktivierbaren auch eine (Na+-K+)-abhängige Transport-ATPase vorkommt.
    Notes: Summary Light- and electron microscopical studies were carried out to demonstrate ATPases activated by Mg++, by (Mg++-Na+-K+), and by Ca++. Histological sections showed clear differences of the activity of Mg++- and Ca++-stimulated ATPases in the light microscope in different layers of the epithelium as well as in different areas of the forestomach. The deeper layers reacted more intensely than the superficial ones. The intensity of the reaction (which depends on incubation time) in the omasal epithelium was stronger than in the lamina epithelialis of the reticulum and much stronger than in the lamina epithelialis of the rumen. In the electron microscope, the reaction products of the ATPase appeared on the outer surface of cell membranes (plasmalemmata). No deposits of the reaction products were observed on those areas of the cell membranes, which are involved in the formation of desmosomes and semidesmosomes. The basal parts of the basal cells were also free from reaction products. As for the distribution and ultrastructural localisation of the deposits, no differences were observed among the ATPase stimulated by Mg++, (Mg++-Na+-K+), and Ca++. Using the technique of Coleman et al. (1967), the cell membranes of ruminal epithelium were isolated. Biochemical assays of the enzymes were carried out. The quantity of cell membranes obtained was 0.3% of the whole homogenate, when compared with 5′-nucleotidase, which is the typical enzyme of plasmalemmata. The biochemical enzyme assays showed that, besides Mg++- and Ca++-dependent ATPases, a (Na+-K+)-dependent transport ATPase exists in the cell membranes of ruminal epithelial cells.
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  • 63
    ISSN: 1432-0878
    Keywords: Intestine, Lampetra fluviatilis ; Serotonin-, dopamine-, noradrenaline-containing neurons ; Identification by histochemistry ; Electron microscopy ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Monoamine-containing neurons in the gut of Lampetra fluviatilis are characterized by histochemical, electron microscopical and biochemical methods. Strongly yellow fluorescent, probably serotonin-containing intrinsic neurons are found along the entire length of the intestine. Their processes aggregate to form large bundles of mainly non-terminal axons, constituting a subepithelial fibre plexus. This subepithelial, ganglion cell comprising plexus is connected to a wide-meshed subserosal plexus which has ganglion cells of different size and few varicose, single axons. Intermingled with both plexus there occur — in the anterior and middle but not in the preanal portion of the lamprey intestine — scattered green fluorescent intrinsic perikarya, emanating faintly green fluorescent, poorly varicosed axons. The formaldehyde-induced neuronal fluorophores conform to serotonin (yellow fluorescent compound), noradrenaline, and dopamine (green fluorescent substance), as revealed in microspectrofluorimetric recordings. The electron microscopical analysis of the yellow fluorescent intrinsic neurons in the terminal hindgut shows nerve cell pericarya and axons equipped with a typical population of occasional small granular and many large granular vesicles (750–1600 Å). The number and opacity of cores of the small and the osmiophilia of the cores of the large granular vesicles are significantly increased following short-term treatment with 5,6-dihydroxytryptamine. Long-term treatment with 5,6- or 5,7-dihydroxytryptamine provokes severe signs of ultrastructure impairment and eventual degeneration in the supposed serotonin-containing axons, besides indications of piling-up of organelles in the non-terminal axons due to arrest of axonal transport. Chromatography of acid extracts from the lamprey intestine, gills and kidney reveals the presence of serotonin (besides another unidentified indoleamine) and dopamine and noradrenaline in the gut, but only dopamine in the brain. The detection of serotonin, noradrenaline and dopamine in the lamprey gut is confirmed by chemical determinations. The occurrence of intrinsic serotonin-, noradrenaline- and dopamine-containing neurons in the gut of Lampetra fluviatilis deviates from the established pattern of innervation of the vertebrate intestine and is considered to be a remnant of an autonomic innervation principle common in invertebrates.
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  • 64
    ISSN: 1615-6102
    Keywords: Insect midgut ; Lipid absorption ; Cytology ; Biochemistry ; Radioactive oleic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Voluntary uptake of triolein, margarine, and lipid-rich natural food (Tubifex) by fasting dragonfly larvae (Aeshna cyanea) led to heavy accumulations of lipid absorption droplets in the enterocytes within 2 days, while subsequent lipid clearance of the midgut epithelium took several weeks depending on the ingested lipid load. No endocytotic lipid uptake was observed after application of a molecular-dispersed fat dye. The smallest lipid droplets first appeared in the subapical groundplasm of the enterocytes and showed a reversible increase in size on their way towards the base. Lipid droplets were also observed at appropriate intervals after oral administration of oleic acid, after feeding margarine in the cold, and after injection of triolein into the isolated midgut. Comparative biochemical analysis after triolein feeding evidenced release of lipase and hydrolytic liberation of FA from TG in the midgut lumen, as well as time-dependent accumulations of TG in the midgut epithelium and of DG in the hemolymph. Oral injection of [14C] oleic acid was followed by its rapid absorption into the midgut epithelium, where it was utilized for the synthesis of MG and esterification to DG and TG. Discharge of radioactive lipid into the hemolymph occurred in the form of FA and DG, while the rectal fat body showed approximately equal labeling of the FA, DG, and TG fractions.
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  • 65
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    Protoplasma 123 (1984), S. 140-151 
    ISSN: 1615-6102
    Keywords: Biochemistry ; Cell wall ; Chitin ; Cytochemistry ; Glomus epigaeum ; Spore
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The cell wall of the spore ofGlomus epigaeum Daniels and Trappe, which has fibrillar subunits regularly arranged in arcs, was studied ultrastructurally and biochemically. The periodic acid/thiocarbohydrazide/silver proteinate (PATAg) reaction for polysaccharide location (Thiéry 1967) and the silver methenamine reaction for protein location (Swift 1968) were performed on whole spores, progressively alkaline-extracted and autoclaved spores, and untreated and alkaline-extracted cell wall fractions. The cytochemical results and those obtained from frozen sections indicated that the fibrils forming the main structure of the outer and inner wall consist of chitin. Quantitative determinations showed that chitin is the most important component (47%) of the alkali-insoluble residue and represents 27.2% of the whole cell wall fraction. It occurs predominantly as the acetylated form. Cytochemical and biochemical observations showed that the matrix surrounding the fibrils is made of alkali-soluble, PATAg positive polysaccharides (4.98% of the whole cell wall fraction). Monomers were identified by gas liquid chromatography as being γ-lactone of glucuronic acid, and glucose, rhamnose and mannose. Alkali-soluble proteins are an important part of the matrix, being spread mostly throughout the inner wall and constituting a large portion (55.1 %) of the alkali-soluble fraction. From the results we derive a model in which the chemical components are interconnected to build up a macromolecular network, in agreement with electron-microscopic observations.
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  • 66
    ISSN: 1432-0878
    Keywords: Gap junction ; Cell junction ; Immunocytochemistry ; Biochemistry ; Heliothis virescens (Insecta)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Subcellular fractions enriched in gap junctions with an ultrastructure similar to those in intact insect tissue have been obtained by extracting crude membranes from the tobacco budworm Heliothis virescens (Lepidoptera: Noctuidae) with 2.5 mM NaOH. n-Octyl-β-d-glucopyranoside (OG) was used to further purify integral membrane proteins in the NaOH-extracted fractions. A polyclonal antibody (R16) is described that specifically labels nonextracted and NaOH-extracted gap junctions in cell fractions by electron microscope immunocytochemistry. R16 immunostaining of sectioned Heliothis testis at the light-microscope level yields a pattern of immunoreactivity consistent with the distribution of gap junctions in the tissue. R16 identifies a 40-kDa protein as a candidate gap junction protein on immunoblots of crude membrane, NaOH-extracted and NaOH/OG-extracted fractions.
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    Journal of comparative physiology 160 (1990), S. 183-186 
    ISSN: 1432-136X
    Keywords: Histology ; Biochemistry ; Muscle physiology ; Hibernations ; Metabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Fiber composition, and glycolytic and oxidative capacities of the pectoralis, gastrocnemius, and cardiac muscles from active and hibernating little brown bats (Myotis lucifugus) was studied. The data were used to test two hypotheses: First, since hibernating bats maintain the capability of flight and make use of leg muscles to maintain a roosting position all winter, the fiber composition of the pectoralis and gastrocnemius muscles should not change with season. Second, we tested the hypothesis of Ianuzzo et al. (in press), who propose that the oxidative potential of mammalian cardiac muscle should increase with increasing heart rate while glycolytic potential should not. Our results indicate that the fiber composition of the pectoralis muscle was uniformly fast-twitch oxidative (FO)_ regardless of the time of year, as predicted. However, the gastrocnemius muscle exhibited a change in FO composition from 83% in active to 61% in hibernating animals. Contrary to the variable change in histochemical properties with metabolic state, a trend of reduced maximal oxidative (CS) and glycolytic (PFK) potential during hibernation in both flight and leg muscles was apparent. The oxidative potential of flight and leg muscles decreased by 15.2% and 56.5%, respectively, while the glycolytic potential of the same muscles decreased by 23.5% and 60.5%, respectively. As predicted, the glycolytic potential of cardiac muscle remained constant between active and hibernating bats, although there was a significant decrease (22.0%) in oxidative potential during hibernation.
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  • 68
    ISSN: 1432-0878
    Keywords: Histamine ; Biochemistry ; Immunocytochemistry ; Retina ; Photoreceptors ; Paraboloid ; Turtle, Pseudemys scripta (Chelonia)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary A combination of immunocytochemical and biochemical methods was used to study histamine in the turtle retina. Histamine-like immunoreactivity was localized within paraboloids of certain cone photoreceptors by use of two different antisera directed against histamine. Preincubation of eyecups in Ringer's containing 10 μM histamine selectively increased the immunoreactivity of these photoreceptor paraboloids. The present localization of histamine in paraboloids indicated that, although histamine is in photoreceptors of the turtle retina, it may play some metabolic or neuromodulatory role, and not function as a neurotransmitter.
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    Cell & tissue research 219 (1981), S. 159-172 
    ISSN: 1432-0878
    Keywords: Seminal vesicles ; Proliferation ; Autoradiography ; Biochemistry ; Rat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Intraperitoneal injection of p-chlorophenylalanine (pCPA) methylester (100 mg/kg body weight) results in an activation of the lysosomal system of the secretory cells in the rat seminal vesicle and an elevation of the activities of lysosomal enzymes within 15 min following the injection. Large autophagic vacuoles are formed, sequestering rough endoplasmic reticulum and part of the Golgi apparatus within 2 h. Shortly after the activation of the lysosomal system an elevation of both DNA and protein synthesis is measured biochemically. 6 h subsequent to the injection a wave of mitoses of the secretory cells begins, reaching a maximum 6 h later and then declining within 3 h. About 12 h following the injection a second rise in lysosomal activity begins, declining within 24 h. The entire sequence of lysosomal and proliferative activities is inhibited in antiandrogen-pretreated rats. Deduced from these findings the following hypothesis of growth regulation of the accessory sex glands is advanced: enhanced loss of intracellular material during autophagocytosis diminishes the intracellular concentration of a substance curtailing cell division below its effective threshold resulting in division of the secretory cells. The prerequisites of this mechanism are (i) a sufficient distributive capacity of the stroma for hormones (androgens) and metabolic precursors, and (ii) sufficient capacity of the basal cells for transporting the precursors to the secretory cells. Sloughing of the secretory cells separates them from these auxiliary structures (stroma and basal cells) and enables the basal cells to divide.
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  • 70
    ISSN: 1432-0878
    Keywords: Intestine ; Sodium transport ; Enterocyte ; Plasma membranes ; Stereology ; Biochemistry ; Cytochemistry ; Domestic fowl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The coprodaeum of the domestic hen maintained on a low-NaCl diet adapts by enhanced sodium transport. This study examines the adaptive response at the single cell and whole organ levels. Surface areas of apical (microvillous) and basolateral plasma membranes of columnar absorptive epithelial cells were estimated by use of ultrastructural stereology. The activities of succinic dehydrogenase (a mitochondrial enzyme) and ouabain-sensitive, potassium-dependent paranitrophenyl phosphatase (a sodium pump enzyme) were determined in tissue homogenates. Sodium, potassium-ATPase (pump enzyme) activity in cell membranes was localized by ultrastructural cytochemistry. Apical and basolateral membranes responded differently. In high-NaCl hens, the membrane signature of the average cell was 32 μm2 (apical), 932 μm2 (lateral) and 17 μm2 (basal). Cells from low-NaCl hens had more apical membrane (49 μm2 per cell) but essentially the same area of basolateral membrane. However, total surfaces per organ were greater for all membranes. Sodium pump enzymes were localized in basolateral membranes. Enzyme activities per unit mitochondrial volume and per unit basolateral membrane surface were higher in low-NaCl birds. These findings are discussed in the context of known mechanisms of transcellular sodium transport via apical ion channels and basolateral pumps.
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    Journal of Computational Chemistry 10 (1989), S. 495-502 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis sets ranging in size from (16, 10, 7) to (20, 14, 11) have been derived for the atoms Y-Cd. Separate sets represent the energy optimized wave functions for each of the s2dn, s1dn+1, and s0dn+2 configurations. The energies from the largest sets are within 3 mhartrees of the values obtained in numerical Hartree-Fock calculations. Reasonable Hartree-Fock s2dn- s1dn+1 and s2dn- s0dn+2 excitation energies may be obtained either using the largest basis sets, or using d-orbitals optimized for the s0dn+2 configurations. The basis sets are slightly unbalanced in favor of the s-functions and in disfavor of the d-functions, but various alternative basis sets may be derived by combining parts of the five parent sets. The convergence of radial expectation values is discussed.
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    Journal of Computational Chemistry 10 (1989), S. 529-551 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
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    Journal of Computational Chemistry 10 (1989) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 74
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Molecular recognition in Rebek's cleft was studied with the MM2 force field. A new computational protocol was used to determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate-receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic π-stacking on the exterior of the cleft.
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    Journal of Computational Chemistry 10 (1989), S. 635-647 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
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    Journal of Computational Chemistry 10 (1989), S. 748-748 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 10 (1989), S. 798-816 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure that finds the most probable conformational states of a protein chain is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. The conformation of the entire chain is represented by a sequence of single-residue conformational states; the distinct conformations in this representation are called “chain-states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain-states. The chain-state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α-helices and ∊-strands of excessive length. The probability estimator considers short-range conformational information, medium-range sequence information and some simple long-range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain-state. By selecting the most probable chain-states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition-based importance sampling minimization.
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    Journal of Computational Chemistry 10 (1989), S. 817-831 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure that generates random conformations of a protein chain, and then applies energy minimization to find the structure of lowest energy, is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. Each state corresponds to a rectangular region in the φ, ψ map. The conformation of an entire chain is then represented by a sequence of single-residue conformational states. The distinct “chain-states” in this representation correspond to multidimensional rectangular regions in the conformational space of the whole protein. A set of highly-probable chain-states can be predicted from the amino acid sequence using the pattern recognition procedure developed in the first two articles of this series. The importance-sampling minimization procedure of the present article is then used to explore the regions of conformational space corresponding to each of these chain-states. The importance-sampling procedure generates a number of random conformations within a particular multidimensional rectangular region, sampling most densely from the most probable, or “important,” sections of the φ, ψ map. All values of φ and ψ are allowed, but the less-probable values are sampled less often. To achieve this, the random values of φ and Φ are generated from bivariate gaussian distributions that are determined from known X-ray structures. Separate gaussian distributions are used for proline residues in the α and ∊ states, for glycine residues in the α, ∊, α*, and ∊* states, and for ordinary residues involved in 29 different tripeptide conformations. Energy minimization is then applied to the randomly-generated structures to optimize interactions and to improve packing. The final energy values are used to select the best structures. The importance-sampling minimization procedure is tested on the avian pancreatic polypeptide, using chain-states predicted from the amino acid sequence. The conformation having the lowest energy is very similar to the X-ray conformation.
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    Journal of Computational Chemistry 10 (1989), S. 856-860 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas are derived for analytical first and second energy derivatives with respect to nuclear coordinates in molecular mechanics force fields employing lone-pair pseudoatoms. These derivatives may further be used for the calculation of normal modes and vibrational frequencies while properly accounting for the presence of pseudoatoms. The equations are applied using the MM2 force field to calculate the vibrational spectrum of methanol to illustrate the applicability of the method. The results are compared to both experiment and a numerical approximation in which small masses are assigned to the lone-pair pseudoatoms.
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    Journal of Computational Chemistry 10 (1989), S. 887-895 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An equation is formulated on the basis of theoretical INDO/FPT calculations which describes the angular dependence of the propanic long-range coupling constant 4JMeH in substituted HCCCH3 fragments. This equation is a truncated Fourier series in the torsion angle φ, HCCMe, which takes into account the dependence of the Fourier coefficients on the bond angle θ, CCMe. The substituent effects are assumed to be additive. Some parameters in the equation may be obtained from the 4JMeH couplings in propane and neopentane derivatives. The calculated effect upon 4JMeH of changes in the bond angle θ is significant and it seems to be in part the cause of some effects which have been attributed to conformational dependence.
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    Journal of Computational Chemistry 10 (1989), S. 911-920 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformations of various cyclic peroxides have been determined using a molecular mechanics force field developed by the authors and previously applied to linear peroxides. Comparison of the results with those of experimental and ab initio studies shows that this force field may be employed without correction for cyclic compounds.
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    Journal of Computational Chemistry 10 (1989), S. 928-934 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article shows that with our Hylleras-functional based method1 for generating correlation orbitals, we can determine electronic structures for small polyatomic systems very accurately. The procedure is ab initio, uses conventional Gaussian basis sets, and solves the electronic Schrödinger equation with the coupled cluster method. A comparison is made with MRCI results obtained in equivalent basis sets for the HF, H2O, and NH3 molecules.
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    Journal of Computational Chemistry 10 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 10 (1989), S. 939-950 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several improvements have been made to the gradient algorithms commonly used to optimize equilibrium and transition-state geometries at the semiempirical level. A gradient algorithm derived from a combination of a variable metric method (Davidon-Fletcher-Powell/Broyden-Fletcher-Goldfarb-Shanno) and Pulay's direct inversion in the iterative subspace method for geometry optimization (GDIIS) is compared with the variable metric method combined with an accurate linear search algorithm. The latter method is used routinely in the standard semiempirical program packages, MNDO, MOPAC, and AMPAC. The combined variable metric and GDIIS algorithm is also compared with GDIIS which uses a static metric. The performance of these algorithms is examined for a wide range of systems with respect to both choice of coordinate system (for cyclic molecules) and guess for the initial Hessian. The results show that the GDIIS method is up to ca. 40% more efficient than the variable metric combined with accurate line search algorithm: however, the exact savings vary depending on the coordinate system and initial Hessian. For noncyclic systems, variable-metric GDIIS is usually equal or superior to static-metric GDIIS, and consistently performs ca. 30% more efficiently than the variable metric combined with accurate line search algorithm. For the optimization of cyclic molecules, an improved estimate of the initial Hessian has increased the efficiency by at least a factor of two. Greater efficiencies (usually 〉40%) are also obtained when static-metric GDIIS is used to refine the geometry after the initial application of a transition-state search based on the variable metric combined with line search algorithm. On the basis of these results, we recommend several changes to the algorithms as currently implemented in the standard semiempirical program packages.
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    Journal of Computational Chemistry 10 (1989), S. 957-962 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article the matrix elements can be grouped into classes by means of the molecular symmetry. By introducing the concepts of symmetry-matrix and symmetry-supermatrix and determining their operation rules, the storage of the supermatrix can be asymptotically reduced by a factor of ca. g2 (g is the order of the molecular symmetry group) and the calculation of Fock matrix during each SCF cycle can be reduced proportionally. Besides, by using the DIIS method combined with the symmetry-matrices, the convergence behavior for highly symmetric molecules can be improved.
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    Journal of Computational Chemistry 10 (1989), S. 975-981 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.
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    Journal of Computational Chemistry 10 (1989), S. 982-1012 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
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    Journal of Computational Chemistry 10 (1989), S. 1031-1037 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A continuum and a discrete-continuum models are used to determine the solvation energies of FCH2COO-, FCH2COOH, and F2CHCOO-. For the anions, the continuum model provides results closer to the experiment, while for the acid, the addition of one water molecule improves the continuum-only energy.
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    Journal of Computational Chemistry 11 (1990), S. 1-18 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Counterpoise corrected ab initio calculations are reported for (H2O)2 and H2O-H2CO. Geometry searches were done in the moment-optimized basis DZP' at the SCF, MP2, and CEPA-1 levels of theory, followed by more accurate single-point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are -4.7 ±0.3 kcal/mol for a near-linear (H2O)2 structure and -4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA-1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
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    Journal of Computational Chemistry 11 (1990), S. 45-57 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A data compression method is presented that is generally applicable to first-order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
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    Journal of Computational Chemistry 11 (1990), S. 67-75 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By examining the displacement coordinate metric three modes of constrained optimization for large molecules and clusters are suggested. The first method corresponds to a conventional optimization using internal coordinates. The second mode has applications with respect to both internal and cartesian coordinates. The final mode is particularly interesting because it can result in computational savings. A mixture of both internal and cartesian coordinates is specified where these coordinates are usually a subset of the molecules or clusters total coordinate set. In the optimization only a subset of the energy derivatives need be evaluated reducing the computational effort associated with the gradient calculation.
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    Journal of Computational Chemistry 11 (1990), S. 159-169 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic potentials calculated from AM1 wave functions have been compared with ab initio STO-3G values and qualitative agreement has been found. Atomic charges derived from AM1 electrostatic potentials for both experimental and AM1 optimized geometries are of comparable quality with STO-3G potential derived charges. These results suggest that the AM1 electrostatic potential may be useful both in its own right and also for deriving atomic charges for use in molecular dynamics studies.
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 663-673 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis set superposition error (BSSE) remains one of the major difficulties besetting current ab initio calculations of molecular interactions. Despite the widespread notion that lowering of the BSSE to negligible magnitude requires extremely large basis sets, we show that simple modifications of basis sets of only moderate size (e.g., 6-31G**) can accomplish the same end at much reduced computational expense. These modifications include reoptimization of the orbital exponents within the framework of the relevant molecules, plus addition of a single diffuse shell of sp orbitals on nonhydrogen centers. Subsequent addition of a second set of d-functions further lowers the SCF BSSE, bringing it below 0.1 kcal/mol for both (HF)2 and (H2O)2. It is notable that addition of the latter d-functions without prior reoptimization of the valence orbitals produces the opposite effect of an increase in the BSSE. Although the MP2 BSSE is also substantially decreased by the above modifications, it appears difficult to reduce this quantity below about 0.4 kcal/mol.
    Additional Material: 6 Tab.
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  • 94
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 674-682 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications of the standard 6-31G** basis set as recommended in the accompanying paper are found to markedly lower the basis set superposition error (BSSE) in the title complexes, in contrast to enlargement to a triple-ζ scheme or by addition of a diffuse sp shell or a second set of d-functions without prior optimization, all of which lead to BSSE increase. After appropriate correction for correlation and superposition effects, all basis sets (with the exception of the standard 6-31G** and 6-311G** with their very large BSSE) predict the cyclic geometry of NH3 dimer to be more stable than the linear arrangement. Correlation and BSSE can shift the equilibrium intermolecular distance in H3CH-OH2 by up to 0.4 Å. Failure to correct for superposition error leads to a drastic exaggeration of both the SCF and MP2 components of the interaction energy in this complex. Much better estimates are furnished by our recommended basis sets with their smaller superposition errors.
    Additional Material: 8 Tab.
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  • 95
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert-Humblet-Rosenfeld (SHR) and the second on the Fano-Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano-Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas-phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.
    Additional Material: 5 Ill.
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  • 96
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 700-717 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The present article addresses the problem of identifying the structure of a parent compound through its chemical fingerprints such as the various numbers of isomeric substitution patterns, along the lines of Kekulé when he arrived at his benzene formula. In a pioneering paper (1929), Lunn and Senior laid out the conceptual framework for the permutation group description of substitution isomerism. It remained, however, for Pólya's celebrated contribution (1937) to initiate the actual mathematical realization of their vision. Pólya supplied the tools for solving the isomer enumeration problem: given a (symmetrical) parent compound, enumerate its spectrum of substitution patterns. The converse problem, though ranked the more interesting one by Lunn & Senior, hardly received any mathematical attention. The present article offers a complete and effective solution.
    Additional Material: 4 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 718-726 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Stereochemistry deals primarily with distinctions based on rigid geometry, e.g., bond angles and lengths. But some chemical species have molecular graphs (such as knots, catenanes, and nonplanar graphs K5 and K3.3) that reside in space in a topologically nontrivial way. For such molecules there is hope of using topological methods to gain chemical information. Viewing a molecular graph as a topological object in space makes it unrealistically flexible; but if one proves that a certain graph is “topologically chiral” or that two graphs are “topological diastereomers,” then one has ruled out interconversion under any physical conditions for which the molecular graph still makes sense. In this paper, we consider several kinds of topological questions one might ask about graphs in space, methology and results available, and specific topological properties of various molecules.
    Additional Material: 12 Ill.
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  • 98
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 727-735 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Hartree-Fock instablities of S2N2 are reported and compared with those of S3N3- and S4N42+. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S2N3, S3N3-, and S4N42+ are of planar C2v type with one of the nitrogens stripped of its π electrons, producing a π hole.
    Additional Material: 13 Ill.
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 100
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To study molecular decomposition pathways it is necessary to use ab initio multireference determinant-configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD-CI (multireference double excitation-configuration interaction technique of Buenker and Peyerimhoff) calculations on the decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
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