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  • Chemistry  (15,132)
  • 2010-2014
  • 1985-1989  (8,169)
  • 1980-1984  (6,963)
  • 1925-1929
  • 1987  (8,169)
  • 1982  (6,963)
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Years
  • 2010-2014
  • 1985-1989  (8,169)
  • 1980-1984  (6,963)
  • 1925-1929
Year
  • 1
    ISSN: 1432-0827
    Keywords: Bacterial amphophile ; Purification ; Chemistry ; Resorption ; Ca influx ; Cyclic AMP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Summary The bone resorptive factor and amphipathic antigen (AcA) previously identified by us in preparations fromActinomyces viscosus have been partially purified, characterized chemically, and compared. They elute at the same location on chromatography with Ac 22. The fatty acid composition of AcA and the bone resorptive factor is the same. Some differences in carbohydrate composition are observed. TheActinomyces factor does not affect calcium influx or cyclic AMP in isolated bone cells. Therefore it is concluded that AcA stimulates resorption either by gaining entrance into bone cells or by way of a yet undetermined second messenger.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Pharmacy world & science 9 (1987), S. 305-314 
    ISSN: 1573-739X
    Keywords: Atrial natriuretic factor ; Blood pressure ; Chemistry ; Diuresis ; Homeostasis ; Kidney ; Muscle, smooth ; Natriuresis ; Receptors, endogenous compounds ; Renin-angiotensin system
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract It is now known that cardiac atria play an important role in blood pressure and volume regulation. Mechanical distension of the atria results in the release of a potent diuretic and natriuretic agent or agents termed the atrial natriuretic factor (ANF). Several structurally related forms of ANF exist in man and it is thought that these represent precursory forms of a single optimally active molecule and/or the presence of more than one form of active ANF. The chemical structure of ANF between different mammalian species is similar. ANF receptors have been identified in kidney, brain, vascular endothelial and smooth muscle cells, tracheal and bronchial smooth muscle and the adrenal glands of many mammalian species, including man. This would suggest that ANF influences blood pressure and volume homoeostasis by affecting any one of a number of biochemical or physiological mechanisms via different target tissues. ANF is now considered a potentially valuable therapeutic agent for the treatment of hypertension and congestive heart failure. Synthesis of potent receptor antagonists could be extremely useful in the treatment of various clinical situations which are produced or complicated by endogenously produced ANF, such as chronic orthostatic hypotension.
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  • 3
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    Electronic Resource
    Weinheim : Wiley-Blackwell
    Angewandte Makromolekulare Chemie 150 (1987), S. 189-192 
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: A morphological study was made to examine the friction and wear mechanisms of ultrahigh molecular weight polyethylene in air and water by means of transmission electron microscopy of a carbon replica film of a very thin layer of the polymer surface slid against a steel ball. Electron diffractions revealed that a molecular orientation with a typical fiber pattern was formed in the friction in air, while thin ribbon-like crystals with particular crystal orientations were formed in water in a way that the sliding took place on the crystallographic a - c plane, giving rise to a low friction coefficient of the polymer.
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  • 4
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    Weinheim : Wiley-Blackwell
    Angewandte Makromolekulare Chemie 150 (1987), S. 137-150 
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Es wurde der relative Wirkungsgrad von fünf handelsüblichen Stabilisatoren bei Photooxidation und thermischer Alterung von Polypropylen (PP) anhand der Änderungen der mechanischen Eigenschaften untersucht. Es wurden Polypropylenproben mit unterschiedlichem Anteil an Cyasorb UV-531 hergestellt (bezeichnet als PC0.5-31, PC1-31, PC1.5-31 und PC2-31). Der Einfluß der Photooxidation auf das thermische Verhalten ist mit Hilfe der Differentialscanningkalorimetrie und durch thermogravimetrische Analysen untersucht worden. 2-Hydroxy-4-n-octyloxybenzophenon (2 Gew.-%) war am wirksamsten, Polypropylen, gegen Verfärbung und Brüchigkeit zu stabilisieren. Bei einer Probe mit 1% Stabilisatorzusatz fanden sich nach 32 h Bestrahlung noch 81% des ursprünglichen Wertes der Streckgrenze gegenüber 18% bei unstabilisiertem PP.
    Notes: The relative effectiveness of five commercially available stabilizers on the photooxidation and thermal ageing of polypropylene (PP) was investigated by following changes in mechanical properties. Samples of PP containing different percentages of Cyasorb UV-531 were prepared (designated as PC0.5-31, PC1-31, PC1.5-31, and PC2-31, respectively). The effect of photooxidation on thermal behaviour was investigated by differential scanning calorimetry and thermogravimetric analysis. 2-Hydroxy-4-n-octyloxy benzophenone (2% w/w) was most effective in stabilizing PP towards discolouration and brittleness. After 32 h irradiation, 81% retention in yield strength was observed in case of PC1-31 against 18% in case of PP.
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  • 5
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    Weinheim : Wiley-Blackwell
    Angewandte Makromolekulare Chemie 153 (1987), S. 113-124 
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Käufliche Weizenmehlstärke wurde unter Verwendung verschiedener Mengen Schwefelkohlenstoff und Acrylnitril xanthogeniert und cyanethyliert und dann zur Herstellung von modifizierten Stärke-Naturkautschuk-Masterbatches eingesetzt. Weiterhin wurden die Einflüsse untersucht, die die Gleichgewichte der Xanthogenierung und Cyanethylierung gegenseitig aufeinander ausüben. Die Ergebnisse werden auf der Basis definierter Wechselwirkungen zwischen der Xanthogenatgruppe und dem freien Acrylnitril erklärt. Hierbei führen sowohl sterische Faktoren als auch die höhere Elektrophilie des Acrylnitrils zum Zerfall der Xanthogenatgruppe. Daher kann die Cyanethylierung nur noch in einem geringeren Ausmaß erfolgen.
    Notes: Common wheat flour starch was subjected to xanthation followed by cyanoethylation at various levels of carbon disulfide and acrylonitrile to prepare modified starchnatural rubber masterbatches. Mutual influences of the extents of equilibrium xanthation and cyanoethylation on each other have been studied. The results have been explained on the basis of a definite interaction between xanthate group and free acrylonitrile in which both the steric factors and higher electrophilicity of acrylonitrile lead to the decomposition of xanthate groups and reduced the extent of cyanoethylation.
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  • 6
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Aus Polychloropren und Polyvinylchlorid wurden Blends in verschiedenen Zusammensetzungen hergestellt und ihre Eigenschaften bestimmt. Die Eigenschaften der Blends zeigen, daß sie Polychloropren in vielen Anwendungen ersetzen können.
    Notes: Blends of polychloroprene rubber and plasticized polyvinylchloride have been prepared in various compositions and their properties evaluated. The properties of the blends show that they can be used to replace polychloroprene in many applications.
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  • 7
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: The present paper describes a rheo-optical apparatus consisting of an elongational rheometer (with rotary clamps) and a device to measure birefringence. This equipment was designed to perform homogeneous deformations on polymer melts in the simple elongational mode. Elongational experiments were performed on polyisobutylene samples at room temperature using different strain rates (from \documentclass{article}\pagestyle{empty}\begin{document}$\dot \varepsilon$\end{document} 0.01 s-1 to 1 s-1). In typical experiments homogeneous elongations up to λ ≈ 200 and stresses up to 2 · 106 Pa were achieved. The stress, the birefringence, and the deformation were obtained by measuring the force, the sample thickness, the optical retardation (the frequency of the sampling was 20 Hz) and the width of the sample (the frequency of the sampling was 3 Hz). It was found that the stress-optical coefficient was constant. The homogeneity of the deformations was carefully controlled because inhomogeneities cause serious errors in the measurements of elongational viscosity and birefringence.
    Notes: Es wird über eine rheo-optische Apparatur zur Verstreckung von Polymerschmelzen mit rotierenden Klemmen berichtet, die mit einer Doppelbrechungs-Meßeinrichtung ausgerüstet ist. Mit dieser Einrichtung können einfache Dehnungen an Polymerschmelzen bis zu hohen Verstreckgraden unter homogenen Bedingungen durchgeführt werden. Während des Deformationsvorganges können die Spannung, die Doppelbrechung und die Probendicke mit einer Meßrate von 20 Hz, sowie die Probenbreite mit ca. 3 Hz erfaßt werden.Wir haben Messungen an Polyisobutylen bei Raumtemperatur mit verschiedenen Dehngeschwindigkeiten (0,01 s-1 〈 \documentclass{article}\pagestyle{empty}\begin{document}$\dot \varepsilon$\end{document} 〈 1 s-1) bis zu einem Verstreckgrad von λ ≈ 200 durchgeführt. Dabei wurden Spannungen bis zu 2 · 106 Pa erhalten. Das spannungsoptische Gesetz war bei homogener Versuchsführung stets erfüllt. Es wird gezeigt, daß ohne Kontrolle der Dehngeschwindigkeit und insbesondere bei inhomogener Dehung nicht nur Abweichungen vom spannungsoptischen Gesetz, sondern auch große Fehler bei der Spannungs- bzw. Viskositätsberechnung auftreten. Deshalb wurde großer Wert auf die Prüfung der Homogenität der Dehnung gelegt.
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  • 8
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    Weinheim : Wiley-Blackwell
    Angewandte Makromolekulare Chemie 153 (1987), S. 187-195 
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: The miscibility of various polymethylmethacrylate (PMMA)/polybutylmethacrylate (PBMA)/poly(methylmethacrylate-co-butylmethacrylate)systems has been studied. PMMA and PBMA are immiscible. Methacrylic homopolymers and copolymers are immiscible, too. A one-phase mixture from PMMA and PBMA is only accessible by copolymerization.
    Notes: Die Mischbarkeit von verschiedenen Systemen aus Polymethylmethacrylat (PMMA), Polybutylmethacrylat (PBMA) und Poly(methylmethacrylat-co-butylmethacrylat) (P(MMA-co-BMA)) wurde untersucht. PMMA und PBMA sind miteinander nicht mischbar. Die untersuchten Homopolymeren und entsprechende Methacrylatcopolymere bilden ebenfalls heterogene Systeme. Einphasige Mischungen aus PMMA und PBMA sind nur über Copolymerisation erreichbar.
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  • 9
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Mit Hilfe der 13C-NMR-Spektroskopie wurde die Entwicklung der Oligomerenverteilung während der Polymerisation von 13C-angereichertem Ethylen mit dem löslichen Ziegler-Katalysatorsystem Cp2TiMeCl/AlMe2Cl verfolgt. Zuordnung und quantitative Auswertung aller Signale der verschiedenen wachsenden Ketten werden beschrieben. Die Geschwindigkeiten der Ethylen- und der Cp2 TiMeCl-Abnahme sowie die Bildungsgeschwindigkeit neuer Ketten konnten direkt aus den Spektren ermittelt werden. So läßt sich zum ersten Mal zeigen, daß die Konzentration der Ti-Propyl-und Ti-Pentylspezies in einen stationthen Zustand einlaufen. Dies ermbglicht, die Geschwindigkeitskonstanten der Ethyleninsertion in die Ti-Kohlenstoffbindung von Ti-Me, Ti-Pr und Ti-Pe zu ermitteln. Diese Ergebnisse fiihren zu einem detaillierten Ein-blick in den Ablauf der ersten Insertionsschritte und sind so eine Grundlage fur die mathematische Modellierung. Sie sind aufierdem ein weiterer unabhlngiger Beweis für die Giiltigkeit des dynamischen Modells des Mechanismus der Ethylenpolymerisation mit lbslichen Ziegler-Katalysatoren, nlmlich die Bildung der polymerisationsaktiven Spezies in zwei aufeinanderfolgenden sehr dynamischen Gleichgewichtsreaktionen.
    Notes: The development of the oligomer distribution during the polymerization of 13C-enriched ethylene by the soluble Ziegler catalyst system Cp2 TiMeCl/AlMe2Cl was followed by 13C-NMR spectroscopy. The assignment of the signals from the growing chains is described in full. It is shown that the rate of consumption of ethylene and Cp2 TiMeCl and the rate of formation of new chains can be monitored directly from the spectra. The concentrations of Ti-propyl and Ti-pentyl species during the polymerization were followed spectroscopically; both attain a steady state concentration. The relative rates were determined for the insertion of ethylene in the Ti-carbon bond of Ti-Me, Ti-Pr and Ti-Pe. These results give a detailed insight into the way that the oligomer distribution develops and provide a basis for its computer simulation. They also provide an independent proof that the dynamic model for the mechanism of ethylene polymerization with soluble Ziegler catalysts of the type Cp2 TiRCl/AlRnClm is correct.
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  • 10
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    Weinheim : Wiley-Blackwell
    Angewandte Makromolekulare Chemie 154 (1987), S. 99-110 
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Der Einfluß verschiedener Reaktionsbedingungen auf die Bromierung von ataktischem Poly(propylen) (APP) in Tetrachlorkohlenstofflösung wurde untersucht. Mit zunehmender Reaktionszeit steigt der Bromierungsgrad. Auch mit steigender Verdünnung der APP-Lösung nimmt die Bromierungsgeschwindigkeit zu, welche bezüglich der APP-Konzentration die Ordnung 0,66 hat. Dies wird erklärt durch die anfängliche Substitution eines Wasserstoffs am tertiären Kohlenstoffatom. Die folgende H-Abstraktion an den benachbaren sekundären und primären Kohlenstoffatomen ist erleichtert. Die scheinbare Aktivierungsenergie wurde zu 11,9 kcal/mol bestimmt. Die Bromierungsgeschwindigkeit steigt bis zu einem APP : Br2-Molverhältnis von 1 : 1 an, darüber hinaus wird die Geschwindigkeit unabhängig vom Molverhältnis. Die Bromierung scheint folgendermaßen zu verlaufen: Nach anfänglicher Substitution eines tertiären H-Atoms durch freie Bromradikale werden nach und nach auchdie sekundäen und primären H-Atome durch weitergehende Substitution oder durch Addition nach einem Eliminierungsschritt ersetzt. Das IR-Spektrum bestätigt die Anwesenheit von Brom in den Proben.
    Notes: Effects of various reaction conditions on bromination of atactic poly(propylene) (APP) in carbon tetrachloride solution were studied. It was found that with the increase of the reaction time the extent of bromination increases. Also with an increased dilution of APP the rate of bromination increased following a bromination order of 0.66 with respect to APP concentration. This has been ascribed to initial replacement of the hydrogen at the tertiary carbon atoms followed by enhanced ease of abstraction from the neighbouring secondary and primary carbon atoms. The apparent activation energy was found to be 11.9 kcal/mol. The rate of bromination increases with an increase of the APP: Br2 molar ratio up to 1 : 1, beyond which the rate becomes independent of this ratio. Mechanism of bromination appears to be an initial substitution of tertiary H-atoms by bromine radicals followed subsequently by replacement of secondary and primary H-atoms via either progressive substitution or elimination-addition. IR spectra confirm the presence of bromine in the samples.
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  • 11
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    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 17-24 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Computer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two-step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.
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  • 12
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    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 79-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aldehydes present in acid-soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin-treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α-chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β-chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
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  • 13
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    Biopolymers 21 (1982), S. 147-157 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe conditions which lead to complete helix formation of poly(I) in the presence of NH4+. Binding of NH4+ is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH4+-poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH4+. A stereospecific model is proposed for the NH4+-poly(I) helix in which the N of NH4+ is located on the axis of the four-stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH4+, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
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  • 14
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    Biopolymers 21 (1982), S. 159-167 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson-Boltzmann theory, is an encapsulating δ-function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson-Boltzmann equation.
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  • 15
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    Biopolymers 21 (1982), S. 203-218 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA-bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron-nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2-3-fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order-of-magnitude increase in their rotational correlation time are attributed to hydrogen-bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
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  • 16
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    Biopolymers 21 (1982), S. 265-275 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dc electrical conductivity of films of the polyelectrolyte complexes of glycol chitosan (GlChi) with the sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) was measured at temperatures above and below room temperature. The maximum field strength in the thinnest film used amounted to 3 × 104 V/cm. A plot of normalized current against the reciprocal of the absolute temperature revealed two regions with different slopes, and activation energies in these two regions have been obtained for all the complexes. The activation energies in the high-temperature region vary from 0.85 to 1.18 eV and in the low-temperature region from 0 to 0.22 eV. Reasons are given to show that the conductivity is probably ionic. Near room temperature, the current-voltage relation is almost linear in the GlChi-DS complex, while in the other three complexes the current varies as a power n of the voltage with the value of n ranging from 1.7 to 2.5. A rise in temperatures causes an increase in the slope of the log I vs log V plot in GlChi-DS and GlChi-CMC complexes. The nonlinear current-voltage relation is ascribed to a space-charge-limited conductivity.
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  • 17
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    Biopolymers 21 (1982), S. 301-319 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Five different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge-shaped crystals) or mannan II (hydrated gel-forming pseudo-fibrillar precipitate). High-molecular-weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low-molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base-plane unit-cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish-kebab structures that were characterized.
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  • 18
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer-water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06-0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption-desorption scanning experiments were performed on a globular protein (α-chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.
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  • 19
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    Biopolymers 21 (1982), S. 451-458 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The light scattering of bovine serum albumin (BSA) has been measured at protein concentration up to 90 g/L and at pH values between 4.4 and 7.6. The dependence of scattering on both protein concentration and pH may be quantitatively accounted for by a simple extension of the hard-sphere model for protein solutions [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol. 112, 437-452] allowing for electrostatic repulsions between molecules. According to the extended model, the radius of the effective hard spherical particle representing BSA varies with the net electrical charge of the BSA molecule in a manner which may be calculated from electrostatic theory.
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  • 20
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    Biopolymers 21 (1982), S. 475-497 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2-Cβ-exo-Cγ-endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.
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  • 21
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    Biopolymers 21 (1982), S. 547-563 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectrum of the enzyme adenylate kinase has been investigated. Theoretical calculations, based on the x-ray crystal structure, have been carried out by means of an origin independent matrix formalism. The entire molecule was included in the calculations in the sense that essentially all electronic transitions that occur at wavelengths longer than 185 nm were included in the basis set. A linear dielectric function was utilized to evaluate the intertransition coupling potentials. The results of the theoretical calculations were in reasonable agreement with experimental CD spectra of the molecule.
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  • 22
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    Biopolymers 21 (1982), S. 633-652 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mode of action of many antitumor agents entails the inhibition of nucleic acid synthesis. Because many of the drugs can intercalate, it is assumed that intercalation is an important step in the mechanism of biological activity. As intercalants contain a planar chromophore as an ingredient essential for intercalation, chromophores that should fit into DNA are desired. This is the main theme of this investigation. Binding to DNA of fundamental moieties, protonated pyridine, aniline, phenol, quinone, and 4H-thiopyran-4-one, is studied to determine their optimum placement in DNA. The optimum orientations for each moiety are superimposed to form polyaromatic systems that can intercalate in a manner in which functional groups on these chromophores are oriented as in the moieties themselves. Ideal intercalants proposed contain three and four fused ring system, have protonated ring nitrogen atoms located to maximize the electrostatic interactions with DNA, hydroxy and amino groups that can hydrogen bond to the OII and O5′ phosphate backbone atoms, and carbonyl and sulfur groups in the central position of the ring system to provide variations in the chromophore and to interact with the relatively positive region in the intercalation site. The optimum orientation occurs when the chromophore and the base pairs overlap to the maximum extent. The ideal intercalants are fundamentally of the type:
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  • 23
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    Biopolymers 21 (1982), S. 665-677 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA reassociation kinetics using the phenol emulsion reassociation technique (PERT) [Kohne, D. E., Levison, S. A. & Byers, M. J. (1977) Biochemistry 16, 5329-5341] has been investigated at high DNA concentrations using an endonuclease S1 assay of reaction progress. Apparent second-order rate constants fall on two intersecting straight lines when presented as a function of DNA concentrations on a log-log plot. In the low DNA concentration range, the rate constants drop about 10-fold when concentration increases 1000-fold. In the high DNA concentration range, the rate constants drop more than 10-fold when concentration increases 10-fold. The slopes of these lines are the same in different solvents and at different temperatures. The intersection between the lines occurs when the available catalytic surface is saturated. At high DNA concentrations, high-complexity heterologous denatured DNA apparently competes 2-4 times better for the surface than homologous DNA because it does not participate in a reassociation reaction. Native and partially native DNA molecules cannot compete with single-stranded DNA for a saturated surface. At high DNA concentrations, reactions using PERT become dependent on the single-strand DNA length. Increasing length lowers reassociation rates.
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  • 24
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 25
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    Biopolymers 21 (1982), S. 859-872 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Classical potential functions (CPF) calculations on 3′-mononucleotides, the building blocks of nucleic acids, predict a correlation between the sugar ring pucker and the torsion angle Φ′ around the C3′—O3′ bond. In ribonucleotides, the value of Φ′ depends on the sugar pucker, viz. the C2′-endo sugar pucker is associated with Φ′ = 210° and 270°, while the C3′-endo sugar pucker favors only Φ′ = 210°. On the other hand, in deoxyribonucleotides, both sugar puckers show a preference for Φ′ = 180°. These theoretical predictions are fully corroborated by the results obtained from x-ray and nmr studies on mono-, di-, and polynucleotides.
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  • 26
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of several surfactants on the secondary structure of bovine β-lactoglobulin B was determined from the circular dichroism spectra. The spectra were measured at several concentrations of surfactant ranging from 1 mg/mL to the critical micelle concentration. The surfactants studied were sodium dodecyl, decyl, and octyl sulfate, sodium dodecyl sarcosinate, dodecyltrimethylammonium bromide. The data were analyzed using the method of Chen et al. [Biochemistry (1974) 13, 3350-3359] to determine the percentage of α-helix, β-sheet, and unordered form at each surfactant concentration. In every case, an increase in structured form and a 20-25% decrease in the amount of unordered form was noted when the surfactant concentration reached the critical micelle concentration. However, the relative amounts of the two structured forms present depend on the surfactant used. The profile of the secondary structure of the protein also varied from surfactant to surfactant as the protein was titrated, probably reflecting the delicate balance between ionic and nonionic forces that governs the secondary structure of β-lactoglobulin and most other globular proteins in aqueous solution.
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  • 27
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amino acids are known to differ in their individual preferences for each of the four positions of the β-turn conformation formed by tetrapeptide segments. Proline and glycine show relatively high preferences for positions 2 and 3, respectively, of the β-turn. Using tripeptides of the type N-acetyl-Pro-Gly-X-OH, where X = Gly, Ala, Leu, Ile, and Phe, we have sought to study the influence of the 4th residue X on the stability of the β-turn conformation in these tripeptides. Our nmr and CD results show that the β-turn stability is quite significantly governed by the nature of the amino acid residue at this position in the following order: Leu 〉 Ala 〉 Ile, Gly 〉 Phe.
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  • 28
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    Biopolymers 21 (1982), S. 1153-1166 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Thermodynamic studies of the binding of adamantanecarboxylate to cyclodextrins have been made as a function of temperature and added organic cosolvent (methanol) using flow microcalorimetry. The negative heat capacity change associated with the adamantanecar-boxylate/β-cyclodextrin interaction and the fact that the interaction is weakened by the addition of methanol implicate the binding process as being a hydrophobically driven one. The negative enthalpy change (ΔH0 = -5.5 kcal/mol) and near-zero entropy change (ΔS0 = 1.5 cal/mol deg) are quite different from the values normally expected for a hydrophobic bond, indicating that other bonding forces are important in addition to the hydrophobic effect. The relative contribution of the hydrophobic effect and other bonding forces (most likely van der Waals forces) to the overall binding was judged from an analysis of the dependence of the thermodynamics of the association process on the surface tension of the water-methanol mixtures following a model for “solvophobic” bonding described by Sinanoglu [Molecular Associations in Biology (1968) Academic Press, New York, pp. 427-445]. From this analysis, adamantane-carboxylate/cyclodextrin complex formation is found to be driven to the extent of -1.9 kcal/mol by the hydrophobic effect. Furthermore, the hydrophobic driving force is found to be characterized by a positive ΔS0 of 10 cal/mol deg. The remaining free energy of binding (and the ΔH0 of binding of ∼-6 kcal/mol) is then due to the intrinsic (surface-tension-independent) van der Waals interaction between the ligand and cyclodextrin cavity.
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    Biopolymers 21 (1982) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 30
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are φPro = -57.8°, ψPro = 139.3°, φAib = 61.4°, and ψAib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.
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    Biopolymers 21 (1982), S. 1333-1363 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The folding-unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only Cα and Cβ atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (φ,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding-unfolding transition for this idealized model is an “all-or-none” type; this is attributable to the specific long-range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding-unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium-range contacts at a β-turn and at the α-helix. (2) These grow to include the native pair of interacting β-strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long-range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.
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  • 32
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.
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    Biopolymers 21 (1982), S. 1469-1472 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 21 (1982), S. 1479-1487 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formalism for extracting the conformations of a proline ring based on the bistable jump model of R. E. London [(1978) J. Am. Chem. Soc. 100, 2678-2685] from 13C spin-lattice relaxation times (T1) is given. The method is such that the relaxation data are only partially used to generate the conformations; these conformations are constrained to satisfy the rest of the relaxation data and to yield acceptable ring geometry. An alternate equation for T1 of 13C nuclei to that of London is given. The formalism is illustrated through an example.
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    Biopolymers 21 (1982), S. 1521-1534 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used broadline proton magnetic resonance to study molecular motion in cellulose, a sodium pectate solution, a calcium pectate gel, and isolated bean cell walls. All samples were prepared in D2O to minimize the contribution of water to the observed signals. For each sample, a free induction decay was obtained, and the second moment, spin-lattice relaxation, and dipolar relaxation were measured. Our results show that the large majority of protons in cellulose are immobile. Rigid and mobile domains were also observed in the pectate samples. We have shown that gelation induces large-scale changes in the free induction decay, the second moment, and the relaxation behavior of the pectate. As with the other samples, rigid and more mobile domains were found in bean cell walls. The fraction in the rigid domains is much larger than the fraction of cellulose in the sample, suggesting that the noncellulosic wall components are also organized into rigid and mobile domains.
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  • 36
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Conformational energy computations were carried out on collagenlike triple-stranded conformations of several poly(tripeptide)s with the general structure CH3CO—(Gly—X—Y)3—NHCH3. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly-X-Pro, Gly-X-Ala, Gly-Pro-Y, and Gly-Ala-Y. Minimum-energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α-aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a —Ch2—CH3 side chain in Abu was mapped as a function of the dihedral angle χ1. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X-Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X-Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple-stranded structure.
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    Biopolymers 21 (1982), S. 1657-1666 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ionization constants of the tyrosyl groups of chymotrypsinogen and of nitrated-chymotrypsinogen (two tyrosyl residues nitrated) have been determined by difference spectrophotometry. In chymotrypsinogen, two of the four tyrosyl groups ionize without any time dependence. Above pH greater than ca. 12.5, time-dependent spectral changes are seen for 0.7 group equivalent. The data can be fitted to the values of pK′1 9.75 ± 0.07, pK′2 11.55 ± 0.05, pK′3 13.30 ± 0.05. In nitrated-chymotrypsinogen, the two nitrated tyrosyl residues have pK′1 6.44 and pK′2 8.30. For both proteins, these pK′ values are in agreement with those evaluated from potentiometric titration and calorimetric data using computer-assisted curve-fitting analysis.
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    Biopolymers 21 (1982), S. 2195-2203 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of several samples of poly(α,β-L-Asp) with a molar fraction of β-bonds ranging from 0.1 to 0.55 was investigated by means of ir and CD spectroscopy and potentiometric titration and compared with the results obtained previously with poly(α-L-Asp). All samples investigated underwent a conformational change induced by changes in their degree of ionization: unpronounced ir absorption of amide V at 650 cm-1 was shifted to 620 cm-1 and substantially increased on deionization; CD spectra changed with the degree of ionization, passing through an isosbestic point; and the pattern of the titration curves was more complex than that of a simple polyelectrolyte. The conformation developing with the decreasing degree of ionization may be considered to be α-helix, as deduced according to the analogous behavior of other polypeptides. The extent of the conformational change in the individual samples depends on the molar fraction of β-bonds: the higher it is, the lower is the helix-forming ability of the sample.
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    Biopolymers 21 (1982), S. 2225-2239 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of 1H-nmr spectroscopy is demonstrated to be a useful analytical method to characterize the structure of synthetic peptides attached to soluble, macromolecular polyoxyethylene (POE) supports in the liquid-phase method (LPM) of peptide synthesis. We report an extensive 360-MHz 1H-nmr study of POE-bound homo-oligo-L-methionine peptides. A combination of high field and selective saturation or Redfield pulse methods allows resolution of individual backbone NH and α-CH resonances of dilute peptides in the presence of strong resonances from macromolecular POE and/or protonated solvents. The nmr spectra for the POE-bound peptides in CDCl3 are qualitatively similar to those of the low-molecular-weight Boc-L-Metn-OMe peptide esters. This corroborates other observations that POE has little effect on peptide stucture. The backbone α-CH region of peptides is overlapped by signals from the terminal oxyethylene group of POE, but the peptide side-chain and low-field backbone NH resonances are well resolved. In trifluoroethanol the Boc-(L-Met)n-NH-POE heptamer and octamer adopt the right-handed α-helical structure, and the present nmr studies provide evidence for two strong intramolecular hydrogen bonds to stabilize the helices. In water, the N-deblocked derivatives, (L-Met)n-NH-POE oligomers adopt β-sheet structure and manifest well-resolved nonequivalent NH resonances with 6-7 Hz 3JNH-CH coupling constants.
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    Biopolymers 21 (1982), S. 2241-2252 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The concerted model of Monod, Wyman, and Changeux is generalized so that all effects of interactions for an enzyme operating at a nonequilibrium stationary state are considered. In contrast to the original model, which is based on an analogy to equilibrium ligand binding, the generalization may show both “positive” and “negative cooperativity” in both catalytic binding and conformational processes. Furthermore, in contrast to any equilibrium binding model, the Hill coefficients may be greater than the number of sites n. For catalysis, the maximum value is 2n, and for conformational changes, n + 1. These points are illustrated by two cases that yield simpler analytic expressions. The first obtains when catalysis occurs on a much faster time scale than the conformational changes, and the second, when this situation is reversed.
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    Biopolymers 21 (1982), S. 2315-2316 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 21 (1982), S. 1473-1477 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 21 (1982) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 21 (1982), S. 1503-1520 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: By combining gel permeation chromatography (GPC) and light-scattering spectroscopy, including photon correlation and angular distribution of absolute scattered intensity, we were able to characterize immunologically active Haemophilus influenzae type b polysaccharide (HIB Ps) bovine serum albumin (BSA) conjugates in terms of equivalent hydrodynamic radius rh ∼ (6.2 ± 0.6) × 102 Å, apparent radius of gyration rg ∼ (5.4 ± 0.3) × 102 Å, apparent molecular weight Mw ∼ (3.5 ± 0.4) × 106 g/mol, and a second virial coefficient A2 ∼ (1.9 ± 0.3) × 10-4 cm3 mol/g2. We could study the effects of each of the processes in the conjugate formation according to the following procedure: BSA (dialysis, modification, fractionation) + HIB Ps → HIB Ps/BSA conjugate (conjugate formation, fractionation). Narrow distributions of HIB Ps BSA conjugate formation can be achieved using fractionated BSA.
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    Biopolymers 21 (1982), S. 1569-1586 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ∼25 to ∼500 cm-1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm-1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm-1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm-1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.
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    Biopolymers 21 (1982), S. 1735-1747 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the oxygen replacement reaction of carbon monoxide-saturated hemoglobin (HbA0) was carried out using spectroscopic, calorimetric, and pH titration methods. Under fully saturated conditions the replacement reaction can be defined by a single partition constant over all ratios of bound oxygen to carbon monoxide. This indicates that under saturating conditions Haldane's first law for the ligand binding of gas mixtures holds for any CO/O2 ratio. It further shows that there is no appreciable difference in relative CO-O2 affinity between the α- and β-chains. The same partition coefficient was found to hold for different pH, buffer, and allosteric effector conditions. The lack of any pH dependence of the partition coefficient was confirmed by the absence of proton changes for the replacement reaction. The temperature dependence of the partition coefficient and calorimetric results yield a value for the enthalpy of the reaction of -3.65 ± 0.29 kcal/mol/heme.
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  • 47
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    Biopolymers 21 (1982), S. 1763-1780 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We demonstrate that the isotropic absorption and linear dichroism in an unknown flow field can be used to determine base tilt in polynucleotides if three transitions are measured and the directions of the corresponding dipoles are known. The method is applied here to reach conclusions about the base tilt in poly(rA), poly(rA)+·poly(rA), and poly(rC). The respective values are: 28° tilt about the axis + 50° toward C8 from the C1′ → N9, and 25° tilt about the axis + 118° toward C5 from C1′ → N1. The results for poly(rA)+·poly(rA) are consistent with the accepted model. Spectra were measured for poly(rC)+·poly(rC), but definite conclusions must await reliable directions for transition dipoles. The dipole direction for the 218-nm transition in rC is found to be +13° or +43° toward C5 from C1′ → N1. The CD spectra to about 168 nm are presented and discussed.
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  • 48
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    Biopolymers 21 (1982), S. 1811-1832 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of stress relaxation in uniaxial extension and associated time-dependent birefringence have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 13-22% fibrin plasticized with either aqueous buffer or glycerol. Both unligated and ligated (i.e., with α-α and γ-γ ligation by fibrinoligase, factor XIIIa) films were studied. Both types showed two stages of stress relaxation, with time scales of approximately 10 and 103-104 s, respectively, with a plateau region between. In the plateau, the nominal (engineering) stress for ligated glycerol-plasticized film is proportional to In λ, where λ is the stretch ratio, up to λ ≅ 2, and it decreases with increasing temperature. For unligated glycerol-plasticized film, the stresses are smaller by a factor of one-half to one-third. For ligated film, the second stage of relaxation is relatively slight, and recovery after release of stress is often nearly complete. For unligated film, the second stage involves a substantial drop in stress, and after recovery there is a significant permanent set. A second relaxation for ligated film reproduces the first, but for unligated film it reproduces the first only if the initial relaxation is terminated before the second stage; otherwise, the second relaxation shows a weaker structure. The behavior of water-plasticized film is similar to that of glycerol-plasticized except that the second stage of relaxation occurs at shorter times. During the first stage of stress relaxation, up to about 100 s, the birefringence and the stress-optical coefficient increase; during the plateau zone of stress relaxation, the birefringence of ligated films is approximately constant and is proportional to 2λ2/(λ2 + 1) - 1, where λ is the stretch ratio. This dependence is predicted by a two-dimensional model in which rodlike elements in the plane of the film are oriented with independent alignment. During the final stage of stress relaxation, the birefringence of ligated films decreases slightly; that of unligated films decreases substantially, but less rapidly than the stress, corresponding to a further increase in the stress-optical coefficient. With additional information from small-angle x-ray scattering reported in an accompanying paper, the first stage of relaxation is attributed to partial release of bending forces in the fibers by orientation, accompanied by increased birefringence. The second stage is attributed, for ligated films, to an internal transition in the fibrin units accompanied by elongation of some of the fibers; and in the unligated films, to a combination of the latter transition with slippage of protofibrils lengthwise within the fiber bundles that causes some loss of orientation, which diminishes the birefringence.
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    Biopolymers 21 (1982), S. 1899-1908 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A microscope capable of measuring the CD of intact single eukaryotic cells, DNA microcrystals, and other microscopic structures has been constructed and tested. It can measure the CD spectra in the 200- and 800-nm wavelength range and consists of a modification to a standard Cary 60 CD machine in combination with a Zeiss uv microspectrometer. Preliminary CD spectra of red blood cells and lymphocytes are presented.
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    Biopolymers 21 (1982), S. 1909-1926 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of fibers in agarose gels has been studied by electron-microscopic examination of replicas formed from freeze-fracture surfaces. For gels set in water, the results obtained support the model proposed for the gel structure by Arnott et al. (1974) of a random array of long, straight, connected fibers, with each fiber having a diameter equivalent to that of an aggregate of approximately 10-30 agarose helixes, depending on the initial agarose concentration. The density of these fibers, their water content, and the total length of fibers per unit volume have been derived from the measured distribution of intersections per unit area of freeze-fracture surfaces. For gels set in the presence of salt, the distribution of fibers becomes distinctly non-Poissonian, leading to larger interfiber spaces and a gel of greater effective pore size. The larger pore size of gels set in the presence of salt also has been revealed by electrophoretic measurements in which the relative migration rates of plasmid DNA molecules of varying conformations have been determined.
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    Biopolymers 21 (1982), S. 1933-1943 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Energy embedding has been shown recently to be a useful extension of the distance geometry approach to conformational calculations in the case of very small molecules and simple energy functions. This paper tests the ability of energy embedding to locate low energy conformations satisfying both weak and strong geometric constraints when the molecule is the small protein, bovine pancreatic trypsin inhibitor, and the energy function is the complicated Oobatake-Crippen residue-residue potential. Using the potential function alone, the algorithm reaches a structure with energy lower than that of the native conformation, but with little resemblance to it. Aided by numerous geometric constraints, such as preformed secondary structure segments, the algorithm again finds a local minimum with energy better than that of the native, and with only 3.3 Å rms deviation from it. This is significantly closer to the native value than can be obtained using standard distance geometry and the geometric constraints alone. Thus, energy embedding using the Oobatake-Crippen potential function is a significant help in finding native conformations of proteins. However, additional trials on a hairpin bend fragment of trypsin inhibitor demonstrate the potential's shortcomings in encouraging proper secondary structure.
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  • 52
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    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 2179-2185].We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche- to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche- to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base-base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.
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    Topics: Chemistry and Pharmacology
    Notes: The microwave absorption of aqueous solutions of DNA extracted from E. coli has been studied between 8 and 12 GHz by the use of an optical heterodyne technique. By measuring optically the temperature rise produced in an absorbing sample by pulsed microwave radiation, unambiguous, direct measurement of the microwave absorption is possible. Our results show that E. coli DNA absorbs microwaves in the 8-12-GHz region substantially more efficiently than water, which is itself an extremely efficient absorber. The observed absorption is featureless and decreases slightly with increasing frequency. These observations are consistent with an explanation involving direct absorption by longitudinal acoustic modes of the double helix.
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    Biopolymers 21 (1982), S. 251-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formation of polyelectrolyte complexes of glycol chitosan (GlChi) with sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) has been studied. The number of ionizable groups per pyranose ring and the degree of dissociation as a function of pH in the polycation and polyanions have been determined using conductometric and potentiometric titrations. The formation of the complexes at different pH values has been followed by turbidity measurements. It is found that stoichiometric complexes of the polycation with CMC, (GalUA)n, and AlgA are formed at a mixing ratio of 0.5, indicating that the conformation may correspond to chains of equal lengths. In the case of the complex of GlChi with DS, the stoichiometric composition corresponds to a mixing ratio of 0.62. Thin transparent films of the complexes have been obtained by dehydration under reduced pressure on a layer of mercury. The dielectric constant ε′ and loss ε″ of thin films of these complexes have been measured in the range of frequencies of 1-100 kHz at different temperatures above and below room temperature. The GlChi-DS complex shows very little change in the values of ε′ and ε″ with frequency or temperature. On the other hand, films of GlChi-CMC and GlChi-(GalUA)n complexes show a significant increase in ε′ and ε″ as the temperature is increased above room temperature. The increase is more prominent at low frequencies. This behavior is attributed to the Maxwell-Wagner interfacial polarization. In the case of GlChi-AlgA film, the values of ε′ and ε″ increase enormously as the temperature increases. This behavior is similar to the increase in ε′ and ε″ observed by Michels et al. [(1965) J. Phys. Chem. 69, 1456-1465] as the salt concentration increases in another polyelectrolyte complex studied by them. The electric double-layer mechanism proposed by Schwarz [(1962) J. Phys. Chem. 66, 2636-2642] to account for the dielectric properties of biocolloids is shown to account quantitatively for the observations on the GlChi-AlgA film.
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    Biopolymers 26 (1987), S. 5-8 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 26 (1987), S. 213-229 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: We present a theoretical basis and new methods for the determination of thermodynamic functions from scanning calorimetry data. A thermodynamic state is defined here as an ensemble of microstates in the system, and it can be defined only through assumptions of its heat capacity function and the two integral constants. With these assumptions, scanning calorimetry data can be analyzed using the single or double (or multi-) deconvolution presented here. New equations to calculate the van't Hoff enthalpy function and the calorimetric enthalpy function are presented. We prove that the agreement of these two functions is a necessary and sufficient factor for the condition that the system can be described with the assumed two-state model.
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    Biopolymers 26 (1987), S. 251-260 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Infrared absorption and ir linear dichroism measurements have been performed on poly[d(A-T)-Cs+] films at various relative humidities. At high relative humidity, samples are in a B form; at low relative humidity, in a C form. The B → C conformational transition is shown to be a noncooperative one corresponding to a gradual evolution of the backbone geometry of the polynucleotide within the B family. the C-form-type spectrum is characteristic of an alternated phosphodiester chain with a dinucleotidic repeat unit.
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    Biopolymers 26 (1987) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 59
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    Biopolymers 26 (1987), S. 403-414 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Molecular mechanical simulations on base-paired deoxyhexanucleoside phosphates, (dAdT)3 · (dAdT)3, (dTdA)3 · (dTdA)3, (dGdC)3 · (dGdC)3, and (dCdG)3 · (dCdG)3, have been carried out to assess their energetic stabilities in left- and right-handed forms. These hexamers have also been simulated with alternating sugar-puckering profiles with the combinations (purine : C2′-endo-pyrimidine : C3′-endo) and (purine : C3′-endo-pyrimidine C2′-endo). The right-handed models have been found to be the energetically most stable structures and the left-handed structures are significantly destabilized. This instability has been rationalized in terms of competition between stabilizing stacking interactions on one hand, and distortions in the bond angles and torsion angles in the sugar-phosphate backbone on the other.
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    Topics: Chemistry and Pharmacology
    Notes: The flexibility of hairpin loops containing n bases (residues) has been examined using a theoretical model [N. L. Marky and W. K. Olson (1982), Biopolymers, 21, 2329-2344] of oligonucleotide loop closure. The study is based on correlated probabilities of chain separation and terminal residue orientation as outlined previously. The probabilities are calculated using standard statistical mechanical methods as functions of local conformational changes of the chain backbone. Our results for an RNA chain of 9 residues suggest that the anticodon loop is a dynamic structure capable of assuming a variety of different spatial conformations. Free energy values related to the various conformations span a narrow range of values (2-4 kcal/mole) and compare well with experimental observations in aqueous solution. Conformational transitions between the loop conformations are within less than 0.5 kcal/mole in free energy. The different spatial loop conformations and the likely pathways between them may have potential relevance to the molecular translation of the genetic code.
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    Biopolymers 26 (1987), S. 463-480 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Secondary-structure prediction has been used to investigate the conformation of the N- and C-terminal telopeptides for type I and type III collagen. The three predictive methods (Chou and Fasman, Robson and co-workers, Lim) indicate mainly aperiodic conformations. A common structural motif is provided by the positioning of β-turns, particularly in the vicinity of the residue sites involved in intermolecular cross-links. An alternative model to that of Helseth et al [(1979) Biopolymers 18, 3005-3014] for the secondary structure of the N-terminal telopeptide of type I collagen is proposed. The general features of these two contrasting structures have been surveyed by model-building techniques employing molecular graphics and energy minimization. The role of the telopeptide component in the structural design of the biomaterial collagen is assessed. Notably, the alternative model clearly serves to demonstrate the compatibility of current cross-linking evidence with the quasi-hexagonal model for the packing of molecules within a collagen fibril.
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    Topics: Chemistry and Pharmacology
    Notes: Conformational analysis from the pattern and intensities of cross-peaks in the two-dimensional nuclear Overhauser effect proton nmr spectra of the homopolymer, poly(dA) · poly(dT), and the analogous oligomer, d(AAAAAATTTTTT)2, indicate that they both exist in the B-conformation. The conformation of the ApT/TpA junction in the oligomer is significantly different from the rest of the base pairs.
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    Biopolymers 26 (1987) 
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    Biopolymers 26 (1987), S. 609-611 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 26 (1987) 
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    Biopolymers 26 (1987), S. iii 
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    Biopolymers 26 (1987), S. 1-3 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 26 (1987), S. 27-43 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The influence of calcium ions on the polymerization induced in fibrinogen solutions by thrombin and by Reptilase has been investigated by meansof static and dynamic light scattering in combination with measurements of the release of the fibrinopeptide A. The calcium concentration was varied in the range between 0.3 and 103 calcium ions per fibrinogen molecule. The enzyme concentration was chosen sufficiently low so that it was possible to make quantitative observations as a function of time, in particular, beforethe onset of gelation. Likewise, the influence of calcium ions on the enzymatically induced polymerization of fragment X was studied. The results indicate that there are at least three mechanisms by which calcium can influence the evolution of the polymer system on the path to gelation and clotting. Which mechanism dominates depends upon the calcium concentration.
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    Biopolymers 26 (1987), S. 17-26 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: We examined the variation in the solvent accessibility and hydrophobicity of the amino acids along the sequences of 58 soluble globular proteins with known tertiary structure. We found that there is a significant tendency for the accessibilities to run in clusters along the sequence but that the hydrophobicities are distributed without such nonrandom clusters. Theseresults suggest severe limitations on the power of sequence analysis tools that use average hydrophobicity scores of overlapping subsequences to predict accessibility.
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    Biopolymers 26 (1987), S. 109-119 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The CD helix bands for infinitely long helical polymers are shown tobe composed of two parts: a derivative-shaped band plus an ordinary Gaussian-like band. The derivative-shaped band results from the zero-order term of an expansion while the Gaussian-like band results from the first-order expansion term. However, the intensities of the two bands are shown to be of the same order of magnitude. They are both linear in the coulombic coupling of transition charge densities for polymer transitions. The sum yields a skewed derivative-shaped band. The shapes of net CD helix bands are shown to not depend on the approximations used for averaging over orientations if the usual systems, such as polypeptides and polynucleotides, are considered in their long-wave-length spectral regions.
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    Biopolymers 26 (1987), S. 137-168 
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    Topics: Chemistry and Pharmacology
    Notes: A procedure, CONGEN, for uniformly sampling the conformational spaceof short polypeptide segments in proteins has been implemented. Because thetime required for this sampling grows exponentially with the number of residues, parameters are introduced to limit the conformational space that has to be explored. This is done by the use of the empirical energy function ofCHARMM [B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus (1983) J. Comput. Chem. 4, 187-217] and truncating the search when conformations of grossly unfavorable energy are sampled. Tests are made to determine control parameters that optimize the search without excluding important configurations. When applied to known protein structures, the resulting procedure is generally capable of generating conformations where the lowest energy conformation matches the known structure within a rms deviation of 1 Å.
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    Notes: The binding of tris(2,2′-bipyridyl)ruthenium(II) cations [Ru(bpy)2+3] with single- and double-stranded (ss and ds) DNA, and the polynucleotides poly(A), poly(C), poly(G), poly(I), poly(I) · poly(C), and poly(U), was studied in aqueous solution. Steady-state electrical conductivity measurements with the polynucleotides, ssDNA, and dsDNA reveal that approximately three nucleotides offer one binding site. This may be compared with the ratio [nucleotide]/[Mg2+] of 2.4 : 1 for dsDNA. After laser excitation (353 nm), the luminescence of Ru(bpy)2+3 bound to nucleic acids shows two decay components. The contribution of the fast component, which is interpreted as resulting from quenching processes of the absorbed ruthenium complex, exhibits a maximum with increasing [nucleotide]/[Ru(bpy)2+3] at a ratio of about three to one. Bound Ru(bpy)2+3 can be released from the strand by addition of NaClO4 [half-concentration: 2.5 and ≤ 10 mM for poly(U) and dsDNA, respectively].
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: One approach to finding the conformation of minimum energy for a complicated molecule is to perform energy minimization, perhaps coupled to more exhaustive search procedures such as dynamics or Monte Carlo sampling, from many starting conformation. Where there are geometric constraints on the conformations, as in a ring molecule, or a variable loop starting and ending in known constant regions of one of a series of homologous proteins, rapidly generating many such starting conformations, all satisfying the constraints, has been a problem in the past. We have devised an algorithm, which we call random tweak, which performs this task in the context of a torsional description of a molecule, and have used it to model the backbones of the six CDRs (complementarity determining regions) of the immunoglobulin MCPC603. These range in size from 5 to 19 residues, and have from 8 to 36 variable dihedral angles. Ensembles of 100 properly closed backbone structures for each CDR were generated under several conditions of van der Waals screening internally and against the rest of the molecule, and ensembles of 1000 were generated for selected CDRs. These structure “libraries” reveal how the geometry at the base of a CDR and the topography of the surrounding protein surface restrict the region of space that a given CDR can occupy. In accord with simple notions of chain molecule statistics, the more highly extended a CDR at its base, the more similar the possible structures and the fewer that are necessary to span the conformational space. Energy minimization and molecular dynamics studies (reported elsewhere) using these libraries to furnish starting conformations show that, as the number of residues in a CDR goes from five to nine, the number of randomly generated structures necessary to ensure that low-lying energetic minima, such as the native conformation, will be found several times goes from a few tens to a few hundred. Some of the spatial features of an ensemble of random conformations are implicit in the histogram of the rms atomic displacements calculated for all the pairs in the ensemble. The random tweak method is carried out by setting each dihederal angle on the main chain of the variable fragment to a random value, then using an iterated linearized Lagrange multiplier technique to enforce the geometric constraints with the minimal conformational perturbation. The time required for the algorithm is linear in fragment length, and the resulting ability of the method to handle large loops makes it especially applicable to the modeling of homologous proteins. In most cases, hundreds of acceptable structures could be generated in a few hours on a VAX 11/780. Where van der Waals screening against fixed atoms need not be performed, as for isolated ring molecules, generation times go down by an order of magnitude or more.
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  • 75
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    Biopolymers 26 (1987), S. 1717-1729 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dynamic light-scattering measurements were carried out for collagen in acetate buffer (pH 4.8) extracted from lathyritic ratskin. The correlation functions were analyzed in terms of the semiflexibility of collagen molecules. The experimental Γ/K2 vs K2 relationship was compared with the theoretical one based on formulation including anisotropy in translational diffusion, chain flexibility, and the hydrodynamic interaction; Γ is the average decay rate and K is the magnitude of the momentum transfer vector. By using the model parameters evaluated from the Γ/K2 vs K2 relationship, a good agreement was obtained between profiles of theoretical and experimental correlation functions over the entire delay times. Detailed examinations of the dynamic light-scattering spectrum permitted us to conclude that a set of the contour length L of 300 nm and the Kuhn length γ-1 of 340 nm are much more probable than other sets of L and γ-1 that equally explain static quantities such as the radius of gyration. The results show that collagen molecules are well characterized by a wormlike chain model.
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  • 76
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied the absorption bands of oxy- and carbonmonoxyhemoglobin in the wavelength range of 650-350 nm (visible and Soret bands) and in the temperature range of 300-20 K. The spectra in the whole temperature range have been successfully deconvoluted in terms of gaussian components. The analysis of the temperature dependence of the first and second moment of the bands enables us to compare dynamic properties of the heme group in oxy- and carbonmonoxyhemoglobin. The results of the analysis indicate that the “mean-effective” frequency of the nuclear motion coupled to the electronic transition responsible for the visible bands is higher in carbonmonoxy- than in oxyhemoglobin. The possible functional relevance of this finding is discussed.
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  • 77
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    Biopolymers 26 (1987), S. 1789-1807 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new static model of enzymatic cleavage of polymeric substrates such as nucleic acids has been derived. The model is compared to that elaborated by Tanford and to experimental data. In predicting the fragment distribution for a restriction enzyme digestion of a circular substrate, the model is superior to that of Tanford.
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  • 78
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 79
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    Biopolymers 26 (1987), S. 1431-1444 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The allowed conformations of the μ-receptor-selective cyclic opioid peptide analog were determined using a grid search through the entire conformational space. Energy minimization of the 13-membered ring structure lacking the exocyclic Tyr1 residue and the Phe3 side chain using the molecular mechanics program Maximin resulted in only four low-energy conformations. These four ring structures served as templates for a further energy minimization study with the Tyr1 residue and Phe3 side chain added to the molecule. The results indicated that the Tyr1 and Phe3 side chains enjoy considerable orientational freedom, but nevertheless, only a limited number of low-energy side-chain configurations were found. The obtained low-energy conformers are discussed in relation to various proposed models of the bioactive conformation of enkephalins and morphiceptin.
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  • 80
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational equilibria of seven methyl β-D-mannobioside conformers have been studied theoretically in five solvents. The structure of each individual conformer has been refined by the PCILO quantum-chemical method from the seven distinct low-energy regions determined from (Φ, Ψ) maps calculated by a potential function method. The stability of the conformers in dilute solution has been evaluated by using a method that consists of electrostatic, dispersion, and cavity terms. The calculated abundance of conformers depends on the solvent and results indicate that the preponderant conformer in the solution may not be the one adopted by mannobiose in the crystalline form. Based on the determined abundance of conformers, thermodynamically averaged nmr parameters, dipole moment, and linkage rotation have been calculated. The solvation behavior of methyl β-D-mannobioside is compared to those previously estimated for cellobiose and maltose.
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  • 81
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    Biopolymers 26 (1987), S. 1509-1526 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nonspecific interaction of the mitogenic lectin Concanavalin A (Con A) with glycosyl-free liposomes of various composition has been investigated by microcalorimetric titration measurements. The results obtained show the following features of main interest: (1) the affinity constants (Ka) of the interaction of Con A with liposomal bilayers are in the order of magnitude 105-106M-1. The reaction enthalpies (ΔH) are positive, and small (approximately 0.1 KJ mol-1 lipid), compared to the free energy terms (-ΔG = 30-40 KJ mol-1 lipid). All lectin-lipid interactions are strongly entropy-controlled (ΔH/TΔS 〈 1.0). These thermodynamic features are characteristic for hydrophobic interaction processes. (2) The liposomal head-group charge does not significantly affect the lipid-affinity of Con A. Electrostatic forces thus appear to play a minor role in lectin-lipid interactions. (3) The lipid affinity of Con A is sensitive to the fluidity of the liposomal bilayers, increasing with increasing fluidity. Below the gel to liquid-crystal phase transition temperature, the lectin binding to liposomal bilayers is inhibited. (4) The binding isotherms, corresponding to the interaction of Con A with liposomes, composed of tightly packed, saturated phospholipids, exhibit pronounced positive cooperativity. This phenomenon is absent in the binding curves, corresponding to the interaction of Con A with more fluid liposomal bilayers. (5) The Con A specific inhibitor α-D-methylmannopyranoside (50 mM) drastically increases the molar reaction enthalpy. The Ka term is significantly reduced in presence of the inhibitor sugar. Urea induces analogous changes in the thermodynamic parameters of the lectin-lipid interaction. The effects of α-D-methylmannopyranoside are thus not Con A specific, but are attributable to solvent effects. (6) It was shown that the binding of one Con A molecule affects a large number (approximately 1000) of phospholipid molecules in the liposomal bilayer. (7) The affinity constants (Ka) of the interaction of Con A with glycosyl-free lipids are smaller by a factor of approximately 10, compared to the Ka terms, reported for Con A binding to biological membranes. The presence of glycosidic receptor groups thus controls the specificity of lectin-membrane interactions, whereas the nonspecific lectin-lipid interactions appear to represent the main driving force for the strong attachment of the lectin to membrane surfaces.
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  • 82
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    Biopolymers 26 (1987), S. 1601-1620 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper, we derive the general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity. Significantly, since the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids. We briefly review how the reduced forms of the general equations have been used by many investigators to evaluate mono- and bimolecular transitions, and then explain how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecularities. We emphasize the strengths and weaknesses of each method of data analysis so that investigators can select the approach most appropriate for their experimental circumstances. We also describe how to analyze calorimetric heat capacity curves and noncalorimetric differentiated melting curves so as to extract both model-independent and model-dependent thermodynamic data for transitions of any molecularity. The general equations and methods of analysis described in this paper should be of particular interest to laboratories that currently are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than two.
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  • 83
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the solid-phase synthesis and conformational analysis of a 14-membered, cyclic enkephalin analog, H—Tyr—c[—D—A2bu—Gly—Phe—D—Leu—] (where A2bu represents α,γ-diaminobutyric acid). The results from the guinea pig ileum (GPI) and mouse vas deferens (MVD) assays show that the analog, though active, has little selectivity for the μ or δ opioid receptors. Conformational analysis is carried out using 1H-nmr and computer simulations, including molecular dynamics and energy minimizations. The results obtained here are compared with the findings of our studies carried out on the μ-receptor-selective diastereomer, H—Tyr—c[—D—A2bu—Gly—Phe—Leu—] [N. Mammi, M. Hassan, and M. Goodman (1985) J. Am. Chem. Soc. 107, 4008-4013]. This comparison allows for insight into the regiospecificity of these cyclic enkephalin analogs.
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  • 84
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Plasma fibronectin is a 450-kD glycoprotein composed of two similar subunits connected by interchain disulfide bridges that may fold over in solution, allowing the amino terminus of each chain to bind the carboxyl terminus of the same subunit or a different subunit, thereby allowing polymerization. In order to study the characteristics of the fold-over interaction, the interaction between the amino terminal 29-kD fragment of fibronectin with native fibronectin has been studied in detail. One 29-kD molecule bound per fibronectin subunit, the apparent equilibrium dissociation constant was 40 nM, and the half-times for association and dissociation at 22°C were, respectively, 16 h and 23 days. Complexation could be inhibited by high concentrations of salt, but not by 8M urea. Amino terminal 20-kD and carboxyl terminal 8-kD subfragments of the 29-kD fragment also bound fibronectin and the activity was dependent on the integrity of the type 1 loop structures. The kinetics of the interaction of 29-kD fragment with fibronectin were unaffected by the presence of ligands, but were affected by detergents such as sodium dodecyl sulfate or deoxycholate, which enhanced the rate of interaction over 100-fold or 6-fold, respectively. Therefore, the interaction of fibronectin with ionic cell membrane components such as deoxycholate in vivo may trigger polymerization.
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  • 85
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    Biopolymers 26 (1987), S. Si 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 86
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    Biopolymers 26 (1987), S. S25 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthesis, spectroscopy, and computer simulations are used in an integrated approach to elucidate secondary structure of oligopeptides. Three lactam-bridge peptides were synthesized and examined. One of these model compounds was shown to prefer a β-turn conformation, as indicated by spectroscopy (CD and nmr), and by computer simulations of minimum potential energy and of molecular dynamics. Partial retro-inverso cyclic analogs of enkephalin were also synthesized and investigated. Biological activity studies of the analogs indicated that the Gly3 carbonyl group and the side-chain orientation of the L-Leu5 residue are important. Hydrogen-bonding patterns for the three analogs are described in terms of the spectroscopic evidence correlated to the molecular dynamics simulations.
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  • 87
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The multiple-minima problem is the most formidable in the conformational analysis of polypeptides. Several approaches have been developed to surmount this problem, and we present an additional one here that may possibly be extendable to very large polypeptides. In this new approach, designated the Self-Consistent Electric Field (SCEF) method, we calculate the electric field, due to the whole molecule, at each CO and NH group of the peptide units, and also in the middle of the C′N peptide bonds, for an arbitrary starting conformation. It is assumed that the native conformation has approximately optimal orientations of its group dipoles in the electric field. The direction of the electric field with respect to the CO and NH bond dipole moments provides information as to which peptide units are the worst oriented. We then compute the changes in the backbone dihedral angles φ and ψ required to align the most unfavorably oriented peptide-unit dipole moments along the electric field. After carrying out such alignment of dipoles, a complete potential energy function is used in a minimization procedure to locate the nearest local minimum. The SCEF and energy-minimization procedures are then applied iteratively to try to locate the global minimum. The effectiveness of this method is illustrated by computations on very different starting conformations of terminally blocked 19-residue chains of poly(L-alanine), for which the global minimum is judged to be the right-handed α-helix.
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  • 88
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nature of the local main-chain conformation of polypeptides with charged side chains has been the subject of considerable discussion since Tiffany and Krimm first proposed [(1968) Biopolymers 6, 1379-1381] that, rather than being random, the chain is locally relatively regular, with conformations similar to that of a left-handed threefold helix. Such structures, referred to as “extended-helix” (EH) conformations, have now been studied in a charged poly(L-glutamic acid) system by a combination of Raman spectroscopy and normal-mode analysis. Calculations were done for EH conformations with 3.0 and 2.4 residues/turn, using force fields refined for α-helix, 31-helix, and β-sheet structures. Together with previous results on the α-helix and β-sheet forms, an interesting new correlation emerged: the frequency of the CαC stretch skeletal mode, usually found in the 900-1000 cm-1 region of the Raman spectrum, is essentially linearly correlated with the value of the φ angle. Applying this relationship to the observed frequencies of the α-helix and β-sheet forms of poly(L-glutamic acid), we find that an observed sharp band in the spectrum of crystals of the calcium salt of poly(L-glutamic acid) (which is close to the frequency observed for the charged form in solution) corresponds to an EH conformation very close to that predicted from energy calculations. These studies thus provide very strong support for our proposal that charged polypeptide chains are not random but adopt local conformations of the EH type.
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  • 89
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    Biopolymers 26 (1987), S. S161 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The time course of a noise signal is not completely random, since it is coupled to the characteristic dynamical behavior of the physical system that produces the noise. The statistical properties of the noise may thus be very informative about the properties of the noise-generating system. The use of the autocorrelation function, of modified autocorrelation functions that show directionality with respect to the time axis, and of probability density-distribution functions of intervals in noise traces are discussed. Thus, by labeling specific points on polymer chain molecules by suitable chormophores between which excitation energy transfer may occur and by analyzing the autocorrelation function of the fluctuations in the emitted fluorescence under steady illumination, one may characterize the internal dynamics of the polymer molecules. It is also shown that the presence or absence of time directionality in noise traces, as tested with the help of some of the above-mentioned statistical functions, may demonstrate whether the noise-generating system is at thermodynamic equilibrium or whether irreversible processes are coupled to the dynamic changes that produce the noise signals.
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  • 90
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    Biopolymers 26 (1987), S. S193 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Salt-promoted adsorption of proteins occurs on hydrophobic gels, on immobilized metal ions e.g., Zn2+, Co2+, Ni2+, Cu2+, and on newly described absorbents provisionally called “thiophilic gels.” The latter gels are characterized by the ligand structure —SO2—CH2—CH2—S—R. In a simple form (R = —CH2—CH2—OH) the “T-gel” is extremely useful for rapid isolation of immunoglobulins from complex mixtures. When R is rich in π-electrons the thiophilic affinity will be superimposed by charge-transfer coupling with hitherto unknown counterligands in interacting proteins. The use of tandem and cascade processes for protein fractionation according to several more or less independent separation parameters is briefly demonstrated.
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  • 91
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    Biopolymers 26 (1987), S. S223 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Microbial polysaccharides have become significant industrial products in recent years, primarily because of their high molecular weight and unique rheological properties. More recently, a new class of microbial biopolymer has been developed - namely, the exopolysaccharide bioemulsifiers. The best studied of this class of biopolymer is the capsular anionic polysaccharide of the oil-degrading bacterium Acinetobacter calcoaceticus RAG-1, emulsan. The emulsan polymer (MW, 106) consists of D-galacatosamine, D-galactosamine uronic acid (pKa, 3.01), and a diamino deoxyhexosamine. The amphipathic properties of emulsan are due in part to the presence of fatty acids linked to the polysaccharide backbone in both ester and amide linkages. Emulsan is characterized by a very high affinity for the oil/water interface, and its major industrial application is in the stabilization of oil-in-water emulsions at very low concentrations (emulsan : oil, 1 : 1000). This interfacial binding is accompanied by a conformational change in the polymer, which in turn allows for the concentration of normally water-soluble cations, proteins, and even phages in the oil layer after emulsion separation. Emulsan is now a commercial product produced by fermentation on an industrial scale. Two major applications are likely to involve its ability to stabilize heavy oil-in-water emulsions for (1) transportation in pipelines of high-viscosity oils at lower temperatures and (2) upgrading of high-viscosity fuels so that the homogeneous oil/water emulsions can be burned directly without water removal. Both applications have been tested on a semi-industrial scale and their feasibility has been demonstrated.
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  • 92
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    Chemie in unserer Zeit 16 (1982) 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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  • 93
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    Chemie in unserer Zeit 16 (1982), S. 35-45 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 16 (1982), S. 69-70 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 16 (1982), S. 94-100 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 16 (1982), S. A32 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 16 (1982), S. 116-123 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 16 (1982), S. A46 
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    Keywords: Chemistry ; Chemistry
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  • 99
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    Chemie in unserer Zeit 16 (1982), S. 149-159 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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  • 100
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Es wurden kationische Polyurethane mit Piperazinringen in der makromolekularen Kette hergestellt. Die Polymeren bilden elastische und lichtdurchlässige Filme. Das Verhalten der verdünnten Lösungen in Lösungsmitteln mit verschiedenen Dielektrizitätskonstanten wurde untersucht.
    Notes: Cationic polyurethanes containing piperazine rings on the macromolecular chain were synthesized. The polymers form flexible and transparent films. The behaviour of diluted solutions in solvents of different dielectrical constants was studied.
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