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  • Chemistry  (15,027)
  • Analytical Chemistry and Spectroscopy  (2,063)
  • Physics
  • STRUCTURAL MECHANICS
  • 1985-1989  (8,571)
  • 1980-1984  (7,523)
  • 1925-1929
  • 1987  (8,571)
  • 1981  (7,523)
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  • 1985-1989  (8,571)
  • 1980-1984  (7,523)
  • 1925-1929
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  • 1
    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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  • 2
    Electronic Resource
    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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  • 3
    Electronic Resource
    Electronic Resource
    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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  • 4
    Electronic Resource
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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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  • 5
    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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  • 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: 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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  • 7
    Electronic Resource
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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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  • 8
    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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  • 9
    Electronic Resource
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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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  • 10
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    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
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  • 11
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    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 12
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    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
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  • 13
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
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  • 14
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    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
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  • 15
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    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
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  • 16
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
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  • 17
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    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
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  • 18
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    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
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  • 19
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    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
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  • 20
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 21
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    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
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  • 22
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    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
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  • 23
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
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  • 24
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    Biopolymers 20 (1981), S. 231-235 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 25
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    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 26
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    Biopolymers 20 (1981), S. 243-247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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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: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
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  • 28
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    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
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  • 29
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
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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: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
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  • 31
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    Biopolymers 20 (1981), S. 2121-2136 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
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  • 32
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    Biopolymers 20 (1981), S. 2137-2142 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
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  • 33
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    Biopolymers 20 (1981), S. 2195-2202 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
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  • 34
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    Biopolymers 20 (1981), S. 2225-2241 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present an alternative to the common lattice model for nonspecific DNA-protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one-dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding-site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee-von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single-stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
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  • 35
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
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  • 36
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
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  • 37
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    Biopolymers 20 (1981), S. 2623-2633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-Nmr was used to measure the rate of cis-trans interconversion of X-Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10-3 s-1 at 25°C was found for the zwitterionic form of H-Ala-Pro-OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10-fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C-terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO-Gly-Gly-Pro-Ala-OCH3 to the closely related cyclic compound c[-Gly-Gly-Pro-Gly-Ala-]. These data are evaluated with regard to their possible use in future studies on the role of X-Pro cis-trans isomerization in the kinetics of protein folding.
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  • 38
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As a model compound for the growing chain in the activated-NCA type of polymerization of α-amino acid N-carboxyanhydride (NCA), 3-[ω-acetylglycyl-poly(α-amino acid) acyl]-α-amino acid NCA (called the prepolymer) having various degrees of polymerization (DPs) was synthesized by the polymerization of Phe, Val, Glu(OEt), and Asp(OBzl) NCA in the presence of AcGly NCA by the tertiary amine. Activated (S)-Phe, Val, Glu(OEt), and Asp(OBzl) NCA were added to the terminal cyclic group of the corresponding (S)- or (R)- prepolymer, and the enantiomer selectivity in the reaction was investigated. With prepolymers having DPs ranging from 1 to 15, the addition reaction always took place preferentially between species having the same configuration, and the degree of the enantiomer selection increased with increasing DP of the prepolymer. With prepolymers having DP = 1 and 2, we found contributions from the chiral terminal unit and the chiral penultimate unit to the enantiomer selection, respectively. Prepolymer having DP = 5 was shown to take a β-type conformation, which led to higher enantiomer selection; and prepolymers having DP = 10 and 15 were shown to take an α-helix conformation, which led to much higher enantiomer selection than did the β-type conformation. In the present investigation the mechanisms of terminal-unit control, penultimate-unit control and conformational control of the enantiomer selection in the activated-NCA type of polymerization were clearly observed.
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  • 39
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The helix-coil transition and conformational structure of poly(8-bromoadenylic acid) [poly(8BrA)] have been investigated using 1H- and 13C-nmr, CD, and ir spectroscopy. The results have been compared with the structure of the related 5′-mono- and polynucleotides. The chemical shifts of H(2′), H(3′), C(2′), and C(3′) nmr signals show an interesting correlation with both the puckering of ribose ring and glycosidic bond torsion angle. Poly(8BrA) shows an upfield shift of the C(3′) signal and a downfield shift of the H(3′) signal compared to the chemical shifts in poly(A). These shifts are consistent with a C(3′) endo-syn conformation for poly(8BrA). A similar effect has been reported previously and is also observed here on the C(2′) and H(2′) signals when the preferred conformation is C(2′)endo-syn (e.g., in 5′-8BrAMP). The chemical-shift parameters thus act as a probe for studying syn ⇄ anti and N ⇄ S equilibria in solutions. The three-bond 1H-′13C coupling constants between H(1′) and C(8) and C(4) have been measured in poly(8BrA) and 5′-8BrAMP and their structural implications have been discussed. The observed preference of a C(3′)endo-syn conformation for poly(8BrA), coupled with other evidence, throws doubt on the validity of a correlation previously reported whereby a syn conformation is associated with a C(2′)endo ribose pucker. The backbone conformation of randomly coiled poly(8BrA) is very similar to the structures found in polyribonucleotides: poly(A) and poly(U). All three polymers show strong preferences for the backbone angles found in RNA helices. The CD spectrum of poly(8BrA) has a striking relationship to that of poly(A). The signs of all extrema are inverted, and the magnitudes are related by a constant factor. We suggest that these differences result from a change in the angle between coupled transition moment vectors in the two polymers. Infrared spectra of poly(8BrA) in H2O and D2O solution are reported for the frequency range below 1400 cm-1. The antisymmetric 〉PO2- stretching vibration is observed at an unusually low frequency in the helix (1214 cm-1). The symmetric 〉PO2- stretch occurs at ∼1095 cm-1 but is not resolved from a ring vibration near this frequency. A conformationally sensitive band, characteristic of helical RNA structures, is observed at 817 cm-1 and disappears when the helix is melted. This observation confirms the conclusion that ordered poly(8BrA) has a regular helical structure with an RNA backbone conformation. A stereochemical explanation is provided for the failure of poly(8BrA) (or other syn polymers) to form double helices with anti-polyribonucleotides.
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  • 40
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    Biopolymers 20 (1981), S. 1103-1112 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The arginine and lysine residues of calf thymus histone H1 were modified with large molar excesses of 2,3-butanedione and O-methylisourea, respectively. Kinetic study of the modification reaction of the arginine residue revealed that the reaction is divided into the two pseudo-first-order processes. About a third (1 Arg) of the total arginine residues of the H1 molecule was rapidly modified without causing any detectable structural change of the molecule, and the slow modification of the remaining arginine residues (2 Arg) led to a loss of the folded structure of H1. In the case of lysine residue modification, 93% (56 Lys) of the total lysine residues of the H1 was modified with the same rate constant, while 7% (4 Lys) of lysine residue remained unmodified. When the reaction was performed in the presence of 6M guanidine-HCl, all of lysine residues were modified. It is concluded that the 2 arginine and 4 lysine residues resistant to modification are buried in interior regions of the H1 molecule and play an important role in the formation of the H1 globular structure, while the other 1 arginine and 56 lysine residues are exposed to solvent.
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  • 41
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    Biopolymers 20 (1981), S. 1191-1209 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molar Kerr constants mK, molar refractions mR, and dipole moments μ are reported for the N-methylacetamides CX3CONHCH3 (X = H, CH3, F. CI, Br) and acetamides CX3CONH2 (X = H, F, Cl, Br). The components of the polarizability tensor α are deduced for N-methylacetamide and acetamide on the basis of the bond additivity approximation. This α is found to be considerably more anisotropic than was indicated in previous determinations by other methods. The data for N-methylacetamide were used to calculate mK, μ, and γ2 (anisotropy squared) of N-acetyl-N′-methylglycine amide and N-acetyl-N′-methyl-alanine amide as functions of the torsional angles (φ,Ψ). The statistical mechanical averages of mK, μ, and γ2 were calculated from conformational energies obtained by the methods of Scheraga.
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  • 42
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    Biopolymers 20 (1981), S. 1247-1260 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The physical properties of single, 5-8-μm diameter, water-swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus (G) has a value of 4.1 × 105 N m-2, the average molecular weight of chains between crosslinks is in the range of 6000-7100, and the stress optical coefficient (C′) is 1 × 10-9 m2 N-1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non-Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7-8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
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    Biopolymers 20 (1981), S. 1333-1335 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 20 (1981), S. 1399-1411 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Heavy meromyosin binding to F-actin saturated with tropomyosin is studied theoretically. The problem is formulated as a special case of n-mer adsorption to a one-dimensional Ising lattice which is divided into m-site-long blocks.
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  • 45
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    Biopolymers 20 (1981), S. 1481-1502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio 〉 20; 0.1 〈 L/P 〈 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
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  • 46
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    Biopolymers 20 (1981), S. 1537-1547 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at 45°C and then leads to a loss of second-order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10-12% in 2.4M Et4NCl fails to increase the acceleration beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35-40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
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  • 47
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    Biopolymers 20 (1981), S. 1503-1535 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: In the preceding article, a Monte Carlo analysis was presented which provides a quantitative numerical relationship between the rotational diffusion coefficients, as measured by the decay of optical anisotropy following an electric field pulse, and the flexibility (persistence length) of short, wormlike chains. In the present article, the results of the foregoing analysis are applied to the observed rates of decay of birefringence for a series of sequenced DNA fragments ranging in size from 104 to 910 base pairs. Under the conditions used in this study, the DNA fragments exist as native, duplex molecules. Furthermore, conditions are defined in which the observed relaxation times are not dependent on DNA concentration, field strength, or the duration of the pulse. It is pointed out that the ionic atmosphere associated with a wormlike polyion does not exert any significant (direct) influence on the rotational diffusion of the polyion and, therefore, that the rotational relaxation times are a true measure of the configurations of the DNA molecules in solution. Moreover, excluded-volume effects are shown not to be significant for the moderately short molecules employed in this study. The major conclusion of this study is that there is no strong ionic strength dependence of the persistence length for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å. For ionic strengths significantly lower than 1 mM, electrostatic contributions to the stiffness of DNA become significant.
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    Biopolymers 20 (1981), S. 1575-1588 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The aqueous and hydroalcoholic solutions of the heptenic macrolide amphotericin B display strong and variable signals in CD and absorption spectroscopies in the range of the π* ← π transition. An interpretation of the spectroscopic changes is proposed based on the equilibrium between two forms of the intermolecular organization: the aggregated one (A) with strong excitonic interaction and the nonaggregative one (B) whose spectra are like those of linear conjugated polyenes in true solution with a well-developed vibrational structure. The intermediate spectra are fitted by linear combination of the A- and B-form spectra. A two-level organization of the aggregates is proposed for the A-form: (1) a close packing of few molecules, which is the origin of the absorption maxima hypsochromic shift; and (2) interaction between the preceding small units inside the aggregates, which is spectroscopically expressed by the intense CD couplet.
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    Biopolymers 20 (1981), S. 1625-1633 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Polypeptides of dicarboxylic amino acids having the monomer units linked in α- and ω-peptide bonds contain two kinds of carboxyls of different acidity. How well potentiometric titration can distinguish these two carboxyls and so characterize the nature of the peptide bonds is evaluated critically. An analysis of the equation describing the dependence of pH on the degree of neutralization based on neglecting the polymer effect and a discussion of the dissociation behavior of polyanions show that the method of evaluating experimental data found in the literature is incorrect. Nevertheless, if a conformational transition does not interfere, some useful and reliable information may be gained by this method; namely, an indication of the presence of two different peptide bonds, their mole ratio, and an approximate pK value for the carboxyl of the amino acid linked in the ω-peptide bond. The presence of two types of carboxyls complicates the evaluation of the titration curves in the conformation studies.
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    Biopolymers 20 (1981), S. 1707-1725 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Conformational analysis of antiparallel double-helical polynucleotides with Watson-Crick base pairing was reduced to a four-dimensional problem using original mathematical methods. In the four-dimensional conformational space the family of structures, characterized by the base-pair stacking with the most stable conformations in water solution as well as in the solid state, was localized. For the C′2-endo sugar pucker, both right-handed and left-handed structures were found; right-handed structures only, however, seem to be allowed for the C′3-endo pucker, the only possible one for ribonucleotides with base stacking.
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    Notes: Angiotensin II and its competitive inhibitor [Sar1, Ile8]-angiotensin II, as well as several analogs of these two compounds specifically chosen for their well-defined pharmacological properties, were studied by circular dichroism and nuclear magnetic resonance methods at various pH values in aqueous solution and in d6-dimethylsulfoxide. The results were compared with their biological activities. This allowed us to establish relationships between conformation and pressor activity, explaining most of the properties of angiotensin II, its inhibitor, and the analogs successively substituted in positions 3 and 5.
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    Biopolymers 20 (1981), S. 2011-2020 
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    Topics: Chemistry and Pharmacology
    Notes: Peptide agonists covalently attached to tobacco mosaic virus exhibit such unusual properties as superpotency, superaffinity, enhanced resistance towards enzymic degradation, and prolonged action at the target cell. These properties can be exploited for the isolation by density-gradient centrifugation of membrane vesicles bearing specific receptors for the peptides and for radioactive and fluorescent labeling of cell-surface receptors. Our observations can be explained by cooperative-affinity phenomena caused by the deployment in space of the agonist molecules.
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    Biopolymers 20 (1981), S. 2035-2049 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The early steps of fibrin aggregation induced by low Reptilase concentrations were studied by means of static and dynamic light scattering. In order to obtain information on the size and shape of the first oligomers, the angular dependence of the scattered intensity and the mean Rayleigh line width were measured. Under physiological pH and ionic strength, oligomer formation was detectable immediately after enzymatic activation. Comparison of the calculated data for different models with experimental results shows that the early fibrin polymerization proceeds as an end-to-end aggregation of elongated and possibly flexible molecules approximately 75 nm long.
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    Biopolymers 20 (1981), S. 2083-2091 
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    Topics: Chemistry and Pharmacology
    Notes: The equivalent conductivity of salt-free solutions of deoxyribonucleates of alkali metals and ammonium obtained by filtering an isoionic DNA solution through a cation exchanger in the corresponding form has been investigated in the concentrations range of 1 × 10-4 to 4 × 10-3M. For all counterions investigated there is a linear dependence of the equivalent conductivity on \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {C_p} $\end{document}, where Cp is the nucleic phosphorus concentration. The limiting equivalent conductivity of deoxyribonucleates increases linearly with the limiting mobility of a counterion. By extrapolation to the zero mobility of the counterion, we have obtained the limiting mobility of a macroion, which is equal to 19 × 10-4 Sm m2 equiv.-1, which is in good agreement with the literature data for denatured DNA obtained by the method of a moving boundary. It is shown that the degree of binding of counterions calculated from the conductometric data in diluted DTA solutions in independent of the nature of the univalent counterion. The degree of dissociation of H+-DNA in the isoionic solution calculated with allowance for the fraction of unprotonated bases practically coincides with this value for salts of DNA. The parameter of Manning's theory calculated from the experimental data corresponds to the distance between phosphates along the chain of the macroion, which is equal to 6.7 Å. We attribute the smaller value of this distance as compared with the theoretical one for denatured DNA to the aggregation of macroions.
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    Biopolymers 20 (1981), S. 2165-2179 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A hydrate of cellulose II can be formed by swelling Fortisan fibers in hydrazine and then washing in water. The hydrate is stable at 93% relative humidity and has a monoclinic unit cell with dimensions a = 9.02 Å, b = 9.63 Å, c = 10.34 Å, and γ = 116.0°; the space group is P21. The unit cell contains disaccharide sections of two chains and approximately four water molecules. The structure was refined using the LALS method, based on 10 observed and 10 unobserved reflections. An antiparallel arrangement of adjacent chains was assumed, since this occurs in cellulose II (the starting material), and the hydrate also reverts to cellulose II on dehydration. Refinement of the positions and side-chain conformations of the chains shows that the chains are stacked in the same way as in cellulose II, and the hydrate is formed by insertion of water molecules between the stacks. However, all efforts to arrange the water molecules in crystallographically regular positions led to unsatisfactory agreement between the observed and calculated intensities. These results suggest an irregular arrangement of the water molecules, which was modeled using water-weighted atomic scattering factors. The analysis resulted in two refined models with relative chain staggers of ∼ +c/4 and ∼ -c/4, which are indistinguishable in terms of the x-ray agreement. Our preference is for the +c/4 model, for which the stacks of chains are analogous to those in cellulose II.
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    Notes: The interaction of calcium ions with α-elastin has been investigated by equilibrium dialysis, CD, and microcalorimetric techniques. Consistent with literature data, it was found that the interaction in water is very poor. In trifluoroethanol (TFE), equilibrium dialysis experiments showed that calcium ions bind to ∼-elastin with an association constant of ∼250 L × mol-1. Such a figure is not consistent with highly specific, highly selective binding. It was also found that the CD response is not directly proportional to the amount of bound calcium but depends on the protein concentration. From microcalorimetric experiments it was found that the heat effect relative to the binding process is of the order of 1.9 kcal/g ion. From this figure and from the binding constant, a positive ΔS value of about 17 e.u. was evaluated, leading to the conclusion that the binding process is entropy driven. From microcalorimetric measurements a ΔH of 1.5 kcal/residue was found for the calcium-induced conformational transition of the protein.
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    Biopolymers 26 (1987), S. 5-8 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 26 (1987), S. 213-229 
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    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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    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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    Biopolymers 26 (1987), S. 403-414 
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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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    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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    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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    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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    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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    Biopolymers 26 (1987), S. 27-43 
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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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    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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    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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    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 75
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    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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  • 76
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    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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  • 77
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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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  • 78
    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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  • 79
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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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  • 80
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 81
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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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  • 82
    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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  • 83
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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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  • 84
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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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  • 85
    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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  • 86
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    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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  • 87
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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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  • 88
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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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  • 89
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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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  • 90
    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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  • 91
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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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  • 92
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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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  • 93
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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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  • 94
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    Chemie in unserer Zeit 15 (1981), S. A4 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 15 (1981), S. 37-45 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 15 (1981), S. 52-61 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 15 (1981), S. 62-67 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 15 (1981), S. coi 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 15 (1981) 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 15 (1981), S. 78-87 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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