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  • Elsevier  (60,017)
  • Wiley-Blackwell  (14,638)
  • American Meteorological Society
  • 2005-2009
  • 1980-1984  (45,443)
  • 1970-1974  (30,730)
  • 1925-1929
  • 1980  (45,443)
  • 1972  (30,730)
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  • 2005-2009
  • 1980-1984  (45,443)
  • 1970-1974  (30,730)
  • 1925-1929
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  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simplified scheme for treating the spatial configurations of polynucleotide chains is developed using the rotational isomeric state approximation and statistical methods applicable to linear systems of interacting subunits. As a consequence of geometric constraints imposed by the skeletal structure and of the severity of certain steric interactions, it is possible to represent the repeat unit comprising six skeletal bonds by two virtual bonds of fixed length. The configuration of the polynucleotide chain as a whole may be conveniently described by an alternating succession of these two virtual bonds. Moreover, analysis of steric interactions suggests that bond rotations governing the mutual orientation of a given pair of successive virtual bonds should be sensibly independent of the rotations affecting the mutual orientation of other pairs. The statistical mechanical treatment of configuration-dependent properties is much simplified in consequence of this mutual independence. Mean-square dimensions calculated by giving equal weights to all sterically allowed conformations are much smaller than values determined by Felsenfeld and co-workers. The calculated dimensions are markedly increased, however, by placing certain arbitrary restrictions on the rotations about selected pairs of skeletal bonds. It is thus demonstrated that steric interactions alone are insufficient to account for the spatial characteristics of polynucleotide chains. The dimensions are also found to be sensitive to the conformation of the ribose ring of each nucleotide unit, but, insofar as the influences of steric interactions are concerned, the dimensions do not depend on the heterocyclic base attached to the ribose ring.
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  • 2
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    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 119-126 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A theory is presented concerning the possible arrangements of protomers in tetrameric molecules. Isoenzymes may exist even in the case of homotetramers if the asymmetry of the identical protomers is detectable. The number of tetrahedral isoenzymes that can be isolated depends on the nature of the intersubunit bonds and on the level of the asymmetry of the protomers. Five isoenzymes can be distinguished only if two different types of protomers form tetrahedral tetramers and the asymmetry of protomers is not detectable with the method used. If the two types of protomers can bind each other by any pairs of binding sets and the asymmetry of both protomer types reaches the level of detection with the method used, we obtain 117 isoenzymes: 15 individual ones, and 51 stereoisomeric pairs.
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  • 3
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    Biopolymers 11 (1972), S. 197-214 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Our previous paper described graphical procedures for evaluating the mode of association in ideal discrete and indefinite cases. This paper concerns the application of such procedures in cases where the non-ideality term BM1 must be considered. Bovine liver L-glutamate dehydrogenase and lysozyme are used as model systems. Several graphical procedures for dealing with cases of 1 - m, 1 - m - n, or indefinite association are developed. The procedure is based on the evaluation of the weight-fraction monomer with-out prior calculation of BM1, using graphical analysis to evaluate the non-ideality term.
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  • 4
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    Biopolymers 11 (1972), S. 271-278 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 5
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preparation of L-lysine peptides (Lysn, n = 2-14) from polyL-lysine is described. Fractionation by ion-exchange column chromatography of poly-L-lysine hydrolysates on a preparative scale resulted in 0.2-1.0 g quantities of individual members of the poly-L-lysine series. The peptides isolated proved to be analytically pure and the optical configuration was fully retained, as demonstrated by complete enzymic digestion. Peptides higher than n = 14 were also prepared. They consisted of oligolysine groups of narrow and accurately determined size distribution. Potentiometric titrations were used both to characterize the products and to demonstrate the characteristic dependence of the dissociation constants on size of the peptide.
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  • 6
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    Biopolymers 11 (1972), S. 549-561 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rate of double helix formation by single stranded Poly A plus Poly U, Poly I plus Poly C, Poly G plus Poly C, and T2 DNA has been investigated as a function of both the length of the reacting strands and temperature. The length dependence of the rate is found to be independent of temperature. All of the reactions studied show a rate approximately proportional to the square root of the length of the shorter of the complementary strands. At or about 30°C below the melting temperature the ribopolymers react with about the same rate. This rate is four to five times slower than DNA renaturation rates. The effect of temperature on ribopolymer reaction rates is interpreted in terms of a steady-state model for helix propagation.
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  • 7
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    Biopolymers 11 (1972), S. 653-659 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: NMR spectra of cyclo(tri-L-prolyl), c-(P)3, show large shifts of the Hα resonance on adding C6D6 to a solution of c-(P)3 in CD2Cl2. CPK models and observed coupling constants indicate a rigid c-(P)3 conformation, independent of solvent composition, suggesting that these shifts result from formation of stereospecific C6D6-c-(P)3 collision complexes in which the c-(P)3 Hα lie near the face of the aromatic ring. The temperature dependence of the Hα shifts and the solvent dependent shifts observed on adding toluene-d8 or nitrobenzene-d5 to the c-(P)3 solution suggest that preferred C6D6-c-(P)3 orientations result from attractive interactions between the electron-rich aromatic ring and the electropositive Hα's and/or δ+ nitrogen atoms in the peptide backbone. Reports of such interactions in increasingly diverse peptide model systems suggest that they may play a role in stabilizing protein structures.
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  • 8
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    Biopolymers 11 (1972), S. 835-847 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Thermal denaturation of native or partially dehistonized nucleohistones shows two melting bands at 66 and 81° in 2.5 × 10-4 M EDTA, pH 8.0. These correspond to the melting of DNA segments bound by the less basic and the more basic half-molecules of histones, respectively. These two melting bands combine into a broad melting band from around 70 to 85° when these nucleohistones are pre-treated with formaldehyde. A formaldehyde reaction which fixes histones on DNA by covalent bonds account for the effect. Formaldehyde fixation also increases the melting temperature of some free DNA segments from around 42 to around 55°. This is interpreted as a result of closed or rigid boundaries between free DNA and formaldehyde-reacted histone-bound DNA segments. MgCl2 dissociates histones from DNA more effectively and leaves longer free DNA segments than does NaCl. Thermal denaturation of a formaldehyde-reacted nucleoprotein thus provides an effective tool for comparing the relative size of free DNA regions on nucleoproteins. The effect of reversible binding of ligands on helix-coil transition of DNA is descussed and found not adequate for thermal denaturation of nucleohistones.
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  • 9
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    Biopolymers 11 (1972), S. 899-912 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The isometric tensile stress generation observed when collagen fibers are immersed in aqueous solutions of lithium bromide ranging in molar concentration up to 7 was studied at 23°C. The reverse process, namely, isometric stress relaxation of the fiber occurring by subsequent immersion in distilled water, was also studied. We find that the data in the region of LiBr concentration up to about 2.5 moles/liter are adequately represented by a superposition integral \documentclass{article}\pagestyle{empty}\begin{document}$$ \sigma (t) = \int_{ - \infty }^\infty {K(t - \tau )} \frac{{dc(\tau )}}{{d\tau }}\,d\tau $$\end{document} where σ(t) is the time-dependent stress generated by the collagen fiber held at fixed length, c(t) is the history of LiBr molar concentration, and K(t) is the isometric contractility function, expressed as stress per unit salt concentration. We conclude that, within a limited range of salt concentration, a collagen fiber in a LiBr bath behaves as if it were a linear, time-invariant system defined mechanochemically by a single function K(t) which depends on the structural characteristics of the fiber while being independent of salt concentration. An analysis is presented of isometric mechanochemical data obtained under conditions of equilibrium by other workers who studied the behavior of collagen fibers in aqueous solutions either of urea, LiBr, or KCNS. The analysis shows that these independent (equilibrium) data confirm the linarity of the relation between isometric contractile stress and salt concentration on which our superposition integral representation is based. We also find that the asymptotic (infinite-time) value of the isometric stress is linearly related to the chemical potential of the salt as well, in agreement with the equilibrium thermodynamic treatment of mechanochemical processes by Katchalsky and Oplatka.
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  • 10
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 11
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    Biopolymers 11 (1972), S. 937-949 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general theory of polyelectrolyte solutions is here used to calculate the differences in Gibbs free energy, enthalpy, and entropy between the coil and helix forms of DNA at any temperature and salt concentration. The salt has univalent cations and is assumed present in excess over the base concentration. The results are restricted to sufficiently dilute solutions. It is shown that the salt concentrations effect is entirely entropic in origin. When applied to the melting temperature, the calculations yield a relation between the enthalpy difference at the melting temperature and the slope of the plot of melting temperature vs. the logarithm of the salt concentration. In accord with observation, both the Gibbs free energy difference at any fixed temperature and the melting temperature are predicted to be linear functions of the log of the salt concentration.However, the theory is not in quantitative agreement with enthalpy data. Data on various colligative and transport properties of both helix and coil forms are reviewed in the text and in Appendix B, and good agreement is found with theory for both forms. No attempt is made to explain why the theory is quantitative for these properties but not for heat measurements.Finally, in Appendix A, an approximate calculation is made of the free energy contributions due to ionic effects not associated with the salt concentration.
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  • 12
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    Biopolymers 11 (1972), S. 1001-1020 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: High-molecular-weight poly-L-alanine dissolved in hexafluoroisopropanol exhibits infrared, ultraviolet, circular dichroism, and optical rotatory dispersion spectra which are unique and unlike any other previously reported polypeptide spectra. Strong evidence that a helical conformation is present is shown by the high degree of hypochromism in the 187mμ absorption peak and by the positions of the amide infrared bands. The CD and ORD spectra are also similar to those of α-helical polypeptides, though important qualitative and qualitative differences are observed. To explain the novel spectra, which are not mixtures of the spectra of previously reported polypeptide conformations, a new α-helix-like conformation is proposed. The postulated conformation (a doubly hydrogen-bonded helix) is a distorted α-helix in which the peptide carbonyl groups point slightly out from the helix axis and are hydrogen bonded simul taneously both to the NH of the fourth peptide residue to the carboxyl terminal side (as in the classical α-helix), as well as to a solvent molecule's hydroxyl hydrogen.
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  • 13
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    Biopolymers 11 (1972), S. 1091-1102 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichriosm (CD) spectra have been calculated for serveral dinucleoside phosphates using a variant of the Pariser-Parr-Pople π-electron molecular orbital method. This method does not require the prior knowledge of the experimental absorption spectra of transition moments of the bases forming the dinucleoside phosphates. Calculated spectra were obtained in good agreement with experimental spectra for four dinucleoside phosphates, ApA, UpU, GpA, and UpA, and reasonable agreement was obtained for ApG and ApU. The effect of changing conformation on the CD spectrum was studied for ApA, UpU, UpA, and ApU; the spectra of UpU, UpA, and ApU were sensitive to small change in conformation, whereas ApA was insensitive over the range of conformation studied. Further studies await detailed knowledge of the structure of dinucleoside phosphates in solution.
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  • 14
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    Biopolymers 11 (1972), S. 1259-1268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solvent-and pH-induced conformational changes are examined in order to investigate the influence of benzyl group. Polymer was prepared via N∊-benzyloxycarbonyl, N∊-benzyl-Nα-carboxy-L-lysine anhydride. The resulting poly (N∊-benzyloxycarbonyl, N∊-benzyl-L-lysine) was obtained in high yield and had a high molecular weight. The protected polymer was removed into poly (N∊-benzyl-L-lysine) by treating it with hydrogen bromide. From the results of the ORD and CD, the protected polymer has a righthanded α-helix, showing [m′]233 = -10,300, [θ]220 = -27,600 and [θ]207 = -25,100 in dioxane. The breakdown of the helical conformation is found to occur at 8% dichloroacetic acid in chloroform-dichloroacetic acid mixture. In the pH range 3.35-6.90, poly (N∊-benzyl-L-lysine) is in a random coil structure. In the pH range 7.50-13.0, the polypeptide has a right-handed α-helix structure; [m′]233 = -12,000, [0]220 = -27,200, and [0]207 = -27,000. In comparison with poly-L-lysine, the coil-to-helix transition is observed at lower pH range in 50% n-propanol. Above pH 8 by heating, the α ⇀ β transition of poly (N∊-benzyl-L-lysine) is not observed in an aqueous media.
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  • 15
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    Biopolymers 11 (1972), S. 1305-1310 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 16
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    Biopolymers 11 (1972), S. 1499-1520 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple sequential model is developed which is applicable to the kinetics of melting of some types of oligomeric helices and as an idealization to the kinetics of unfolding of some protein molecules. A procedure is presented for calculating the concentrations of all conformational species as functions of time. The time course of experimentally observable quantities which depend on these concentrations may then be computed.One of the most characteristic features of the model is the distinction between a transient and a steady-state phase. During the latter all molecular parameters change at the same rate, which depends strongly on the difficulty of nucleation and the length of the sequence. Simple approximations to the steady-state rate are discussed in terms of the exact solution. Rates of transient processes dependless strongly on the rate of nucleation and the number of steps and are a more direct reflection of the rates of the rates of the elementary process of propagation. The value of experimental observation of transient process is emphasized.
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  • 17
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    Biopolymers 11 (1972) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 18
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    Biopolymers 11 (1972), S. 1593-1605 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Far-infrared spectra were measured for the sequential copolymers of amino acids with alkyl group side chains. The analysis of the spectra showed that (L-Ala-L-Ala-Gly)n, (L-Ala-Gly)n, (L-Ala-Gly-Gly)n, (L-Val-L-Ala-L-Ala)n, and (L-Val-L-Ala)n, have the antiparallel pleated sheet structures and that the backbone conformations of (L-Val-L-Val-L-Ala)n and (L-Val-L-Val-Gly)n are the same as that of poly-L-valine. The far-infrared bands characteristic of the antiparallel pleated sheet structure were assigned on the basis of the result of the normal coordinate analysis of poly-L-alanine with this structure. The intersheet and interchain spacings of the sequential copolymers with the antiparallel pleated sheet structure were determined from the x-ray powder-diffraction patterns of these samples.
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  • 19
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    Biopolymers 11 (1972), S. 1583-1592 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroism spectra of acridine orange bound to E. coli tRNA were studied at varying tRNA phosphate-to-dye (P/D) ratios for both unfractionated and purified materials in the absence of Mg++. From the rather discrete features exhibited in the circular dichroism spectra three types of interactions were observed: (1) A high P/D ratio such as 75.2 or 49.8 indicates the interaction between the nucleotide base and dye molecule. The spectra with a large positive peak at 515 mμ are, however, quite different from that of DNA-AO complex under similar conditions. (2) With an intermediate P/D ratio (26.5 to 9.6) dye molecules bound strongly to the polynucleotide chain. (3) With low P/D ratios (≤7.5) the interaction appears to be due to the stacked dye molecules in the single-stranded part of tRNA. The spectra of the third group have an isobestic point at 477 mμ. Below a P/D ratio of 4 the spectrum shows one positive and two negative bands which may be the characteristics of circular dichroism of stacked dyes in polynucleotide chain.Although no drastic change in the conformation of tRNA itself was detectable in the presence of Mg++ in the ultraviolet region, a dramatic change was observed in the circular dichroism of tRNA-acridine orange complex when Mg++ concentration was increased to 10-3M. It was inferred that certain conformational changes other than simple hydrogen bond formation occured in tRNA molecules at this high Mg++ concentration, so that the amount of bound dye in the stacking condition was increased through the transition.
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  • 20
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    Biopolymers 11 (1972), S. 1607-1612 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly (L-Prolyl-Glycyl-L-Prolyl), a polymer which resembles collagen by physical and immunochemical criteria, has been shown to serve as a substrate for the highly specific bacterial collagenase obtained from Clostridium histolyticum. The postulated reaction products Gly Pro, Gly Pro Pro, and Pro Gly Pro Pro have been isolated. The enzyme has been employed as an analytical tool in elucidating the sequence of synthesized polymers of proline and glycine.
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  • 21
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Apparent second-order rate constants for complex formation between poly (I) and poly (C) and copolymers of C containing non-complementary I or U residues have been determined spectrophotometrically. The rate constants decrease as the concentration of either I or U in the C strands increases-the effect seems insensitive to the species of residue involved, when differences in the thermal stabilities of the poly (I) poly (C,I) and poly (I). poly (C,U) complexes are taken into account. These results suggest that low concentrations of relatively stable defects can alter the apparent kinetic “complexity” of polynucleotides as determined by hybridization methods (C0t analysis).
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  • 22
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    Biopolymers 11 (1972), S. 1661-1684 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA which has been heat denatured in the presence of Cu++ ions can be completely and rapidly renatured by increasing the ionic strength of the solution above a critical value. A kinetic study of this renaturation recation was carried out by following the associated UV absorbance change and also by following the change in free Cu++ ion concentration by means of a specific Cu++ ion activity electrode. The data obtained could be fitted to first-order kinetics for a considerable extent of the reaction and the rate constant was found to increase with temperature and ionic strength, but to decrease markedly as the bulk viscosity of the solution was increased. At temperatures greater than 5°C the reaction rate depended on the time elapsing between denaturation and the commencement of the renaturation reaction. As there was good agreement between the rate constants obtained by following the decrease in hyperchromism and by following the increase in free Cu++ ion concentration, it is concluded that under the conditions employed, the rate of renaturation is determined by the rate of release of Cu++ ions from the denatured DNA-Cu++ complex.
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  • 23
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    Biopolymers 11 (1972), S. 1723-1744 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational aspects of a series of copolymers of L-Leucine and L-leucine [poly-(LysxLeuy)] containing 0 to 0.41 mole fraction L-leucine have been studied by circular dichroism (CD) and potentiometric titration in 0.05M KF solution. CD studies on the α-helical conformation showed a dependence of the magnitude of the CD ellipticity band at 222 nm on copolymer composition; the [θ]222 decreasing with higher leucine contents. This was interpreted as the result of an increase of the hydrophobicity of the environment of the amide group due to the presence of the leucyl residues. Values of the Zimm-Rice parameter, σ, for the copolymers were obtained from the potentiometric titrations and used to fit theoretical curves to the experimental data. Using the variation of σ with polymer composition, a value of σ for the leucyl residue was estimated to be 6.3 × 10-2, assuming independence of σ on the amino acid sequence in the copolymer. The free energy change for the conversion of one mole residue from uncharged helix to uncharged coil, ΔGhc°, was also obtained from the titration data for each copolymer up to a leucine mole fraction of 0.16; a value of 385 cal mole-1 was estimated for ΔGhc° for a leucyl residue. These values for σ and ΔGhc° are compared with other values in the literature for various amino acid residues obtained from titration and melting curve data.
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  • 24
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    Biopolymers 11 (1972), S. 1745-1763 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Optical rotatory dispersion measurements were used to follow the transition from the helical to the random coil conformation of poly-β-benzyl-L-aspartate as induced by changes in temperature and solvent composition in mixtures of dioxane and dimethylsulfoxide. Within experimental error, there is no difference in the stability of the helical state as measured in this way for the protonated and deuterated forms of the polypeptide. This result is considered in terms of previous attempts to study the isotope effect on conformational transitions of helical biological macromolecules and polypeptides. The conclusion is drawn that the apparent changes in conformational stability observed in these previous systems arise from alteration of the properties of the solvent. Speculations are advanced regarding the contribution of the interpeptide bond to the stability of the helical state.
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  • 25
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The helical structures of poly[(S)-thiazolidine-4-carboxylic acid], in the cis and trans forms, were redetermined by using the new sets of bond angles and bond lengths established by X-ray diffraction analysis of L-thioproline. Calculations of the helical structures of poly-L-proline and poly[(S)-oxazolidine-4-carboxylic acid] were also repeated. As a result of these energy calculations, it is suggested that, in contrast to poly-L-proline and poly[(S)-oxazolidine-4-carboxylic acid], poly[(S)-thiazolidine-4-carboxylic acid] should not mutarotate from the trans to the cis form. This result is due to the fact that the energy barrier for the conversion is most likely too high. Previous experimental work is consistent with this finding.
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  • 26
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of optical rotatory dispersion (ORD) and circular dichroism (CD) were made in the range of 400-205 nm for polysaccharide tribenzoates such as 2,3,6-tri-O-benzoyl amylose (I), 2,3,4-tri-O-benzoyl dextran (II), tri-O-benzoyl pullulan (III), 2,3,6-tri-O-benzoyl cellulose (IV), 2,3,6-tri-O-benzoyl mannan (V), and polyglycan dibenzoates such as 2,3,-di-O-benzoyl amylose (VI), cellulose (VII), and mannan (VIII). All compounds exhibit Cotton effects in the region of their UV absorption bands (206-285 nm).Comparison of the corresponding di- and tribenzoyl polysaccharides shows a qualitative agreement in number, position and sign of the CD bands but differences in ellipticity magnitude. The disubstituted derivatives exhibit smaller amplitudes than the trisubstituted ones. The contribution of the C(6) chromophore (linked by a CH2-group to the asymmetric C(5) atom) was determined to be of the same sign as the combined contribution of the C(2) and C(3) substituents.The CD bonds of the individual polysaccharide derivatives, which differ in number, sign, and position, were discussed in terms of the steric position of the single chromophores and the steric arrangement and interaction caused by the configuration of the polysaccharides. The optical behavior of these polysaccharide derivatives was found to be not strongly influenced by a definite chain conformation in solution.
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    Notes: The influence of the substituents upon the Amide I and νNH frequencies has been analyzed for ten amides substituted by aliphatic side chains. By considering the aliphatic chain field effect, some data are obtained as to the conformation of the N—Cα bond. In two amides, the presence of an equilibrium between two conformers is shown and a semiquantitative estimation of the energies involved is obtained. The consequences for polypeptides conformation, especially for poly-L-valine, are discussed.
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  • 28
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    Biopolymers 11 (1972), S. 2079-2090 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The effect of dielectric constant (D) of the solvent on the viscosity of heparin was examined using the relation \documentclass{article}\pagestyle{empty}\begin{document}$ \eta _{{\rm sp}} /c = [\eta ]_\infty (1 + k/\sqrt c) $\end{document}, where [η]∞ is the shielded intrinsic viscosity obtained by extrapolating \documentclass{article}\pagestyle{empty}\begin{document}$ \eta _{{\rm sp}} /c\,{\rm vs}{\rm . }\,1/\sqrt c ) $\end{document} to infinite concentration, and k is an interaction parameter independent of the dielectric constant of the solvent. This equation was previously reported by the authors9 for describing the reduced viscosities of strong polyelectrolytes in salt-free polar solvents. It was found that the [η]∞ of heparin increases linearly with increasing dielectric constant of the solvent whereas the k values were, within experimental error, independent of D in the range 54.7 〈 D 〈 93.2 examined. Graded hydrolysis of heparin from its acid form (heparinic acid) at 57°C resulted in samples of varying degree of desulfation with corresponding decrease in biological activity. It was found that both [η]∞ and k decrease with increasing desulfation.
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  • 29
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    Biopolymers 11 (1972), S. 2171-2177 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Density gradient analysis of purified lambda phage particles after storage reveals that minor species with new banding desities arise during storage. These have densities expected for phage-ghost clusters containing integra rations of ghosts to phage particles. A lage numbersof new banding species has been observed.
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  • 30
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    Biopolymers 11 (1972), S. 2191-2194 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 31
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    Biopolymers 11 (1972), S. 2223-2231 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The high-humidity X-ray pattern of oriented fibers prepared from salmon spermheads strongly resembles that of DNA in the B form. However, the nucleoprotamine pattern has a more intense first layer line and increased lateral unit-cell dimensions.Complexes of DNA with poly-L-lysine and poly-L-arginine were prepared and photographed at various relative humidities. The most crystalline patterns were obtained at 92% and also indicate DNA in the B form. However, whereas polylysine-DNA, like the spermheads, has a primitive hexagonal cell, polyarginine-DNA, like NaDNA, has three molecules in the unit cell. Polylysine-DNA, but not polyarginine-DNA, also resembles spermheads in having a strong first layer line.All three complexes show increasing intermolecular distance with increasing humidity, but with sharp maxima when photographed in water, which indicates cross-linking between the molecules. Lowering the humidity causes the polylysine-DNA, but not polyarginine-DNA, to change conformation from the B to the C form.The structural implications of these results are discussed in the light of model-building studies and a comparison of calculated and observed X-ray intensities.
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    Biopolymers 11 (1972), S. 2233-2240 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The pH, temperature, and reagent concentration dependences of the cyanuration of tyrosines within proteins are compared with those of the free amino acid. The results indicate that the mechanism of the cyanuration reaction is a nucleophilic aromatic substitution of the SN2 type, where the tyrosine oxygen acts as a nucleophile and the displacement takes places at a carbon atom which is part of the six-membered ring of the s-triazene. This reaction must compete with the hydrolysis of cyanuric fluoride in aqueous media. These competing reactions generate curves for the pH dependence of the reactivity of tyrosine with cyanuric fluoride whihc vary in a predictable manner with the extent of ionization of tyrosine and the concentration of cyanuric fluoride. In the case of proteins, the dependence of the degree of tyrosine reactivity on pH and temperature within the pH range of full reactivity of the free amino acid reflects constraints imposed by the microenvironment of these groups within the three-dimensional structure of the macromolecule.
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  • 33
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    Biopolymers 11 (1972), S. 2197-2221 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Serum albumin undergoes a conformational change at pH 4, known as the N-F transition. In the customary Linderstrøm-Lang treatment of hydrogen ion titration, the carboxyl groups in serum albumin either have an abnormally low pK, or are buried in charged form, and the Linderstrøm-Lang charging parameter ω decreases dramatically at the N-F isomerization. In the present paper partition functions are derived and distribution functions are calculated for a model permitting salt bonding between the positively and negatively charged sites on a macromolecule. The N-form has an abnormally high salt bonding constant whereas that of the F-form corresponds to that of small ions. The result obtained is consistent with a “normal” intrinsic pK of the carboxyl groups of serum albumin without burying of any charges and with an unchanged ω. The nature of the postulated salt bonding is discussed.Further, it is shown that the “abnormal salt bonding” of serum albumin can explain its unusual ability to bind anions. Theoretical binding curves are calculated and compared with literature data of the Cl- binding of serum albumin. The relation of the present model to other models of hydrogen ion and anion binding to proteins is discussed. Some additional consequences of the present model are pointed out; a transition in the alkaline range, analogous to the acid transition, seems probable. Literature data support the existence of such a transition but do not allow detailed calculations at present.A general, thermodynamic treatment of the interactions between small ligands and macromolecules is outlined. Important points are the choice of the statistical-me- chanical ensemble and considerations of the fluctuations about the mean bonding, if (i) there are not only a ligand-locus interaction but also interligand interactions (in par- ticular intdigand attraction), or (ii) there is a conformational change in themacromole- cule depending on the ligand binding. In these cases, the binding isotherms obtained from thermodynamically closed systems (canonical ensemble) may erroneously indicate a distribution about a single probability maximum, i.e., the statistical mean binding N̄, and fluctuations about this value. The description of a phase change in a bound phase or a change in the “internal” self-interactions of a macromolecule requires a bind- ing equation permitting distributions about two maxima, i.e., (i) N1* 〈 N̄ (“thin” phase) and N2* 〉 N̄ (“condensed” phase) or (ii) two macromolecular conformations P′, and P″, having occupancy numbers N̄, and N̄2, respectively. The N-F transition is an example illustrating the relation between the complete distribution functions and the two-state approximation.
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  • 34
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    Biopolymers 11 (1972), S. 493-507 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Three samples of poly-γ-benzyl-L-glutamate have been prepared from γ-benzyl-N-carboxy-L-glutamate anhydride with n-hexylamine initiation at anhydride-to-initiator molar ratios, [A]/[I], of 3, 4, and 8, and their conformation and association in ethylene dichloride and dioxane have been investigated by means of infrared spectra and vapor-pressure osmometry. Two conformations, σ-and β-forms, are present in those solvents, and the content of β-form increases with increasing A/I value and concentration. At infinite dilution molecular association is absent, but the number-average molecular weight increases with cocentration, markedly in ethylene dichloride and, to a lesser extent, in dioxane. The fraction of residues involved in associated molecules have been estimated as a function of concentration. Combination of the content of β-structure with the fraction of association leads to the following results. The A/I 3 and 4 polymers form intermolecularly hydrogen-bonded aggregates, in which hydrogen-bonded residues are in the β-structure. The A/I 8 polymer has the intramolecularly hydrogen-bonded β-structure at very low concentrations, but it also forms intermolecularly hydrogen-bonded aggregates at high concentrations.
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    Biopolymers 11 (1972), S. 527-528 
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  • 36
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    Biopolymers 11 (1972), S. 587-605 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Dielectric studies have been carried out for the helix-coil transition of poly-β-benzyl-L-aspartate with m-cresol as a solvent. The transition of the solute molecules has been sharply reflected as a characteristic change in the dielectric dispersion curves in changing temperature. Two polarizations, one having a low and the other a high critical frequency, have appeared. According to theoretical considerations of a model of a broken helix, the former is found to come from the orientation. of helical sequences and the latter from the chemical relaxation due to the helix-coil transition. It also seems likely that the unfolded chain may have a polarizability which could not be neglected at the high-temperature side of the transition.
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    Topics: Chemistry and Pharmacology
    Notes: Circular Dichroism measurements have been carried out on poly-L-lysine (PLL) and on random copolymers of lysine and phenylalanine at various pH values and in the presence of different amounts of NaClO4. The results indicate that either the homopolymer or the copolymers at pH conditions at which the side-chain amino groups are fully protonated, assume the right-handed α-helical conformation in the presence of NaClO4. The results are interpreted in terms of specific binding of ClO4- ions on charged side-chain amino groups.
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    Biopolymers 11 (1972), S. 667-678 
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    Topics: Chemistry and Pharmacology
    Notes: Thermal denaturation of DNA's and the corresponding helix-coil transformation of artificial polyribonucleic and polydeoxyribonucleic acids have been studied extensively both theoretically1-13 and experimentally. 14-30 Much less work has been carried out on the properties of these polynucleic acids at high pressure, and in particular, on the presure dependence of the helix-coil transition temperature.31-33 Light-scattering techniques have been used in this study to measure the pressure dependence of the helix-coil transition temperature of the two- and three-stranded helices of polyriboadenylic and polyribouridilic acids and of calf thymus DNA. From the slopes of the transition temperature vs. pressure curves and heats of transition obtained from the literature,20,34 the following volume changes from these helix-coil transitions have been obtained: (a) -0.96 cc/mole of nucleotide base pairs for the poly (A + U) transition, (b) +0.35 cc/mole of nucleotide base trios for the poly (A + 2U) transition, and (c) +2.7 cc/mole of nucleotide base pairs for the DNA transition. The relative magnitudes and signs of these volume changes which show that poly (A + U) is destabilized by increased pressure, whereas poly (A + 2U) and calf thymus DNA are stabilized by increased pressure, indicates that further development of the helix-coil transition theory for polynucleotides is needed.
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    Biopolymers 11 (1972), S. 735-735 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 40
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    Biopolymers 11 (1972), S. 745-759 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Helix-coil transition curves are calculated for poly (dA) poly(dT) and poly (dA-dT) poly (dA-dT) using the integral equation approach of Goel and Montroll.5 The transitions are described by the loop entropy model with the exponent of the loop entropy factor, k, remaining an arbitrary constant. The theoretical calculations are compared with experimental transition curves of the two polymers. Results indicate that the stacking energies for these two polymers differ by about 1 kcal/mole of base pairs. Also, a fit between theory and experiment was not possible for k 〉 1.70.
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    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism spectra of many natural DNAs and double-stranded synthetic polynucleotides were obtained. The eight first-neighbor contributions to the CD spectra of a DNA have been extracted from these data. Therefore, the CD spectrum for any DNA with known first-neighbor frequencies may be easily calculated. For a natural DNA the CD spectrum may be approximated by assuming the first-neighbor frequencies have the most probable values consistent with the base composition. Under favorable conditions, the measured CD spectrum can be used to determine thirteen of the sixteen first-neighbor frequencies of a DNA to ± 0.02 mole percent. The TG, CA, and TA first-neighbor cannot be unambiguously resolved by our method. The accuracy of the first-neighbor frequency analysis depends on the number of different first-neighbors present in the DNA and the extent to which they differ from the most probable value.The extinction coefficient at 260 nm and the base composition can also be calculated from the CD spectrum.
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  • 42
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    Biopolymers 19 (1980), S. 823-831 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The effect of the DNA-binding oligopeptide distamycin A on the B to A transition of DNA in ethanol/water solutions has been studied by means of CD. (The overbars indicate that it does not matter which particular form of the corresponding families is considered.) The results show that increasing the concentration of distamycin A reverses the A conformation (in 82% ethanol) to the B conformation due to its strong binding and stabilization of the latter. In accordance with previous data for pure aqueous solutions, a site size of 3.5 base pairs is obtained from the studies in water/ethanolic solutions. From the data on the B to A transition in the presence of distamycin A, we estimated the length of the cooperativity ν0 = 10 base pairs.The results demonstrate that the oligopeptide systems of distamycin, as well as those of netropsin, are effective stabilizers of the DNA B-conformation.
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  • 43
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    Notes: Tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N-terminal side, were studied in their various ionic states in 2H2O and in Me2SO-d6 by 1H- and 13C-nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H-1H, 13C-13C, and 13C-1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β-turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3JC3αH-N3H and the 3JC2′-H3α coupling constants, which both furnish a dihedral angle of φ3 = -90°, and from the positive value of the temperature coefficient of the glycine-4 amide protons, which suggests a type 4 → 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side-chain rotamer fractions of the residue in position 3. In the β-turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β-turn.
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    Topics: Chemistry and Pharmacology
    Notes: An algorithm is presented for the Monte Carlo simulation of the decay of fluorescence polarization from segmentally flexible molecules. Based on the random walk model of Brownian motion, the treatment explicitly follows the stochastic changes in the diffusion coefficients as the molecule bends. It includes the effects of a linear restoring force opposing the bending and the effects of hydrodynamic coupling between the translational, rotational, and bending motions. One application is presented: the simulation of anisotropy decay curves for hinged rods. A variety of decay curves are obtained, including single- and multiexponential behavior, and the following conclusions are reached: (1) increasing the flexibility is usually, but not always, accompanied by a more rapid rate of depolarization; (2) reducing the size of the fluorescent subunit will usually, but not always, increase the rate of depolarization; and (3) the complex interplay between the effects of molecular shape, relative sizes of the subunits, restoring force, and orientation of the transition dipoles renders it unlikely that any simple method can be used to interpret anisotrophy data without simulation. In particular, it is not possible to determine the extent of bending by fitting the data with the two-exponential approximation used by some investigators in the past.
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    Biopolymers 19 (1980), S. 977-990 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C-nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C-nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6-anhydrogalactose), and the positions of the sulfate and O-methyl groups in a polysaccharide molecule.
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    Topics: Chemistry and Pharmacology
    Notes: The dielectric response of human umbilical cord hyaluronic acid in various environments has been studied at microwave frquencies using a resonant microwave cavity as a probe. Both the real and imaginary parts of complex dielectric constant and the loss tangent for hyaluronate solutions are obtained by utilizing equations for perturbation of a resonant cavity. Dielectric changes at room temperature have been observed in aqueous solutions of hyaluronic acid as a function of concentration ranging from 0 to 350 mg/ml. The data indicate the existence of ordered phases in hyaluronate solutions at selective concentrations, that is, exhibiting lyotropic-type transitions. Hyaluronate solutions at 1.5 and 3 mg/ml concentrations have been studied at various pH in the range of 6-8 and at constant ionic strength 0.1. A temperature-dependent transition in hyaluronate solution of 120 mg/ml concentration has been observed at physiological temperature. It is shown that this temperature-dependent behavior can be related to the orientational polarizability term in the Debye theory of polar molecules in liquids.
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    Biopolymers 19 (1980), S. 945-964 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In 1974, Zimm described a theory which predicts that the sedimentation coefficient of high-molecular-weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed-dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well-defined sucrose-gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T-even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild-type phage (T4D+) was also used in some experiments.In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.The results show that in the range of 25,000-50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed-dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.
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    Topics: Chemistry and Pharmacology
    Notes: The fixation of cis (NH3)2Cl2Pt(II) to poly(I)·poly(C) leads to the formation of two complexed species. One involves coordination to a single base (accounting for about 70% of the total platinum bound over the rb range 0.07-0.25) and the other to two bases which are not adjacent to each other but may be on the same strand and separated by a loop. Reaction of the platinum compound with poly(I) gives in addition to the above two species a minor one (about 15%, independent of rb over the range 0.05-0.30) in which the platinum is bound to two adjacent bases. The availability of such coordination reduces the dominance of the 1:1 species, which, however, remains the major one (ca. 55%).
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    Biopolymers 19 (1980), S. 1329-1344 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The complex of CH3Hg(II) with the accessible cysteines of glyceraldehyde-3-phosphate dehydrogenase (GAPD, EC 1.2.1.12) from rabbit muscle has been studied by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The wavelength dependence of the phosphorescence decay kinetics has also been measured. Comparison of CH3Hg(II)-GAPD with GAPD by these methods shows that a specific optically resolved tryptophan site of GAPD is perturbed by the interaction with a nearby mercury atom. The perturbation on the luminescence and ODMR properties is typical of an external heavy-atom effect. Based on the x-ray diffraction structure of the lobster enzyme, it is proposed that the heavy-atom effect results from the interaction of tryptophan-310 with CH3Hg(II) bound to cysteine-281 in the rabbit muscle enzyme.
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    Biopolymers 19 (1980), S. 1415-1434 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The energy of interaction of a spermine molecule with the A- and B-forms of DNA has been calculated, assuming that the molecule of spermine is fixed in the narrow groove of the DNA helix with the formation of hydrogen bonds between the amino groups of spermine and the phosphate groups of DNA. The atom-atom potentials method was used. Optimal structures for the A-DNA-spermine and B-DNA-spermine complexes are suggested. It is shown that, in agreement with the experimental data, the interaction of the spermine molecule with the A-DNA is energetically more favorable than that with the B-DNA. Two main factors are responsible for this: (1) the distance between neighboring phosphates of the chain in A-DNA (which is about 1 Å less than that in B-DNA) corresponds better to the distance between the amino groups of the propyl part of spermine; and (2) the orientation of phosphate groups in A-DNA inside the groove is preferable for complex formation with spermine to the outside groove arrangement of the phosphates in B-DNA. These conclusions are further confirmed by the calculations for DNA-propane diamine complexes.
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  • 51
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analog of valinomycin, cyclo[-(D-Ile-Lac-Ile-D-Hyi)3-] (C60H102N6O18), has been determined by x-ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds N—H…O=C, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso-valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L-Lac residues, the less crowded face.
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  • 52
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    Biopolymers 19 (1980), S. 1555-1566 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Possible conformations of lacto-N-tetraose, lacto-N-neotetraose, related disaccharides, and other milk oligosaccharides have been studied by an energy-minimization procedure using empirical potential functions. Lacto-N-tetraose favors a “curved” conformation, while lacto-N-neotetraose favors an approximately “straight” conformation. These two conformations differ mainly in the position of the terminal galactose residue with respect to the rest of the molecule. This difference explains the greater strength of lacto-N-neotetraose compared with lacto-N-tetraose in its ability to inhibit the cross-reaction of blood group P1 fractions with Type XIV pneumococcal antipolysaccharide. Although the favored conformation of lacto-N-tetraose (inactive) agrees with the model proposed by the earlier workers, that for lacto-N-neotetraose (active) differs. The favored conformations for the disaccharides galactose-β(1-4)-N-acetylglucosamine, galactose-β(1-3)-N-acetylglucosamine, and lactose are similar in overall shape, differing only in the nature and orientation of the side groups. This explains their nearly equal inhibitory activity. These theoretical models also explain the increased activity of lacto-N-fucopentaose I over that of lacto-N-tetraose and the relative activities of the substituted lactoses. The present studies suggest that it is the overall shape of the molecule which is important for activity, rather than the terminal β(1-4)-linked galactose residue alone.
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  • 53
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    Biopolymers 19 (1980), S. 1571-1585 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C spin-lattice relaxation times of poly(L-lysine) have been obtained at 67.9 MHz in aqueous solution and in a mixed solvent (40% methanol/60% water). A concomitant determination of the conformation by CD permits the correlation of conformation and rotational diffusion of the polymer. The dependence on pH of the spin-lattice relaxation times of the 13Cα and the side-chain carbon resonances reflects the diffusional motion in the random-coil conformation, in the helix-coil transition, and in the conformation of the α-helix. In the mixed solvent the reorientational correlation time of the Cα-Hα vector increases from τ = 0.37 nsec (random coil) to τ = 12.0 nsec (α-helix). In aqueous solution the correlation time of this vector increases from τ = 0.33 nsec (random coil) to τ ≫ 11 nsec. The reorientation rates of the side-chain methylene groups in the two solvents are markedly different. The reorientation of all methylene groups is reduced in the mixed solvent.
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  • 54
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solid-state conformation of copolymers of β-benzyl-L-aspartate [L-Asp(OBzl)] with L-leucine (L-Leu), L-alanine (L-Ala), L-valine (L-Val), γ-benzyl-L-glutamate [L-Glu(OBzl)], or ∊-carbobenzoxy-L-lysine (Cbz-L-Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700-250 cm-1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L-Asp(OBzl)] induces a change from the left-handed into the right-handed α-helix. This conformational change for the poly[L-Asp(OBzl)] copolymers was observed in the following composition ranges: L-Leu, 0-15 mol %; L-Ala, 0-32 mol %; L-Val, 0-8 mol %; L-Glu(OBzl), 3-10 mol %; and Cbz-L-Lys, 0-9 mol %.
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  • 55
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    Biopolymers 19 (1980), S. 1667-1673 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dry purified ligamentum nuchae elastin has been investigated for physical aging. The samples were quenched from a temperature (197°C) close to the softening point to a number of measuring temperatures ranging from -20 to +180°C. At each temperature, the small-strain torsional creep properties were determined at a number of elapsed intervals after the quench. Aging effects were found over the whole temperature range, and the creep and aging behavior of elastin turned out to be very similar to that of synthetic polymers.
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  • 56
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 57
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    Biopolymers 19 (1980), S. 1705-1713 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Covalently closed circular DNA can exist in different configurations known as circular, toroidal, and interwound. Changes among these forms can be made in several ways, including the insertion of dye molecules between adjacent base pairs, which tends to untwist the double-helical structure. The aim of this paper is to discuss these configurations, and the changes among them, in the context of classical elastomechanics. The concepts of twisting, linkage and writhing are explained. Simple experiments on a twisted linear-elastic rod are described, and it is shown that although the circular and interwound forms may be modeled in this way, the toroidal form does not occur, being mechanically unstable. Theoretical energy calculations by Levitt on bent and twisted DNA show that DNA exhibits a particular kind of nonlinear elasticity in which there is an unusual coupling between bending and twisting. The aim of the paper is to show qualitatively that this special kind of elasticity can stabilize the toroidal form of closed circular DNA.
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  • 58
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    Biopolymers 19 (1980), S. 1357-1374 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light-scattering, viscosity, and sedimentation experiments on aqueous solutions of k-carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long-range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer-Fixman analysis, giving a value for the Mark-Houwink coefficient under theta-conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark-Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light-scattering radius. The relations between molecular parameters are corrected for the poly-dispersity of the sample.
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  • 59
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    Biopolymers 19 (1980), S. 1407-1414 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 60
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    Biopolymers 19 (1980) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 61
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    Biopolymers 19 (1980), S. 1475-1489 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An approximate analytic expression for the translational friction coefficient of a toroid modeled as a continuous shell of frictional elements is derived using the Kirkwood approximation. The accuracy of this expression was determined by comparing the friction coefficients predicted by it to those predicted by extrapolated shell-model calculations using the modified Oseen tensor. To show that these calculations do indeed yield the correct friction coefficients, actual translational friction coefficients were determined by observing settling rates of macroscopic model rings or toroids in a high-viscosity silicone fluid. Our conclusion is that the approximate expression yields friction coefficients that are about 1.5-3% low for finite rings. For thin rings, a comparison is also made with the exact result of Yamakawa and Yamaki [J. Chem. Phys. 57, 1572 (1972); 58, 2049 (1973)] for the translational friction of plane polygonal rings. This comparison shows that the approximate expression yields results which are low by 2-3% unless the rings are extremely thin, in which case the error is larger. In the limit of an infinitely thin ring the approximate expression reduces to the Kirkwood result [J. Polym. Sci. 12, 1 (1954)], which is low by 8.3%. We discuss briefly how this work may be useful in determining the structure of DNA compacted by various solvent-electrolyte systems and polyamines.
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  • 62
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    Biopolymers 19 (1980), S. 1451-1474 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Internal Brownian motions of clean φ29 and λ-DNAs have been studied using photon-correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm-2, can in every case be satisfactorily simulated by a Rouse-Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single-strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single-strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single-strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse-Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light-scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.
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  • 63
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    Biopolymers 19 (1980), S. 1507-1515 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman spectra of polyribouridylic acid excited in the uv region, from 363 to 290 nm, are reported. The conformational changes of the polymer from random coil to ordered structure with stacked bases at high and low temperature, respectively, are reflected by important changes in the Raman line intensities; this Raman hypochromism is itself a function of the excitation wavelength - its profile has been determined and shows negative values in the region of 290 nm (near resonance), i.e., hypochromism becomes hyperchromism. Thus the knowledge of the hypochromism excitation profile is important in following order-disorder transition of a polymer using resonance Raman spectroscopy. Theoretical attempts are proposed for explanation, involving not only the relative variations of the molar extinction coefficient on the order-disorder transition of the polymer, but also the damping factors of the vibronic levels. The theoretical curve is found to fit adequately the experimental data over the excitation range, using only the frequency of the O-O transition of uracil and a vibronic linewidth of 2200 cm-1.
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  • 64
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    Biopolymers 19 (1980), S. 2177-2190 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preferential interaction of sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) with the solvent components in water/2-chloroethanol mixtures has been determined using density-increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2-chloroethanol and at constant chemical potential of 2-chloroethanol. Sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2-chloroethanol-induced coil-to-helix transition of sodium poly(α-L-glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α-L-glutamate) is solvated by one 2-chloroethanol molecule. The location of water and 2-chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.
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  • 65
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    Biopolymers 19 (1980), S. 2223-2245 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complex formation between tryptamine and mononucleotides and dinucleoside phosphates containing adenine and/or cytosine has been studied at five pD's ranging from 1.1 to 7.4 by proton magnetic resonance spectroscopy. Chemical shifts of base ring protons and the ribose anomeric proton in the nucleotides and indole ring protons in tryptamine were monitored and their changes with pD and intermolecular interactions interpreted qualitatively. Stacked complexes were found to exist at all pD's in the range studied. Complex geometries differ depending on pD. An electrostatic interaction between the tryptamine amino group and the nucleotide phosphate group contributes to complex formation above pD 4 but is not strong enough to shift the dinucleoside phosphate equilibrium towards the unstacked conformer.
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  • 66
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical conformational energy calculations have been carried out for N-methyl derivatives of alanine and phenylalanine dipeptide models and N-methyl-substituted active analogs of three biologically active peptides, namely thyrotropin-releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone-releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N-methylated residue is in the trans configuration show that (1) N-methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around φ = -135° ± 5° and ψ = 75° ± 5°, and (3) the αL conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C5 (extended) conformation is second lowest in energy. When the peptide bond (ωi) is in the cis configuration the ith residue is energetically forbidden in the range φ = 0° to 180° and ψ = -180° to +180°. Conformations of low energy for ωi = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the αR conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low-energy conformers are found for [(N-Me)His2]TRH. These conformers differ only in the φ and ψ values at the (N-Me)His2 residue. Among the different low-energy conformers found for each of the ENK analogs [D-Ala2,(N-Me)Phe4, Met5]ENK amide and [D-Ala2,(N-Me)Met5]ENK amide, one low-energy conformer was found to be common for both analogs with respect to the side-chain orientations. The stability of the low-energy structures is discussed in the light of the activity of other analogs. Two low-energy conformers were found for [(N-Me)Leu7]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D-Ala6,(M-Me)Leu7]LHRH is considered.
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  • 67
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Based on steric and electrostatic considerations, the prerequisites for binding to DNA via the intercalation mechanism are proposed. Steric contour energy curves are presented to demonstrate the region inaccessible to an intercalant. They are calculated with a 6-n (n = 14) potential. This method is a soft potential analog of an excluded-volume approach. Electrostatic contours on the steric surface illustrate the relatively positive and negative regions of the binding site. The principal intercalation sites, predicted to fit into B-DNA via a tetramer-duplex unit, and the unconstrained dimer-duplex units, obtained in crystal structures, are examined. These contours illustrate the requirements of size, conformation, and net atomic charges necessary for intercalation and optimum binding. Based on the limited space available for intercalation by the presence of the backbone and the maximum base-pair separation of 8.25 Å, an Essential Metabolite Exclusion Hypothesis is presented.
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  • 68
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the near-uv CD spectrum of lysozyme was carried out in the presence and absence of the inhibitor tri-N-acetylglucosamine, and theoretical chiroptical calculations based on the tetragonal crystal structure of the enzyme and the enzyme-inhibitor complex were performed. The results of these calculations indicate that the near-uv CD spectrum of lysozyme can be adequately explained in terms of negative rotatory strengths arising from the tryptophan 1La (293-300 nm) and the disulfide n-σ* bands (250 rm), and positive rotatory strength contributions from the tryptophan 1Lb bands (291 nm) and the tyrosine 1Lb bands (275 nm). Contributions to the rotatory strength of each band were approximated in terms of specific interactions between chromophores. It was found that the rotatory strength of most of the near-uv transitions arises primarily from coupling interactions involving other side-chain chromophores and amide groups which are in close proximity. Changes which are observed in the lysozyme CD spectrum on binding of tri-N-acetylglucosamine may be explained in terms of changes in the rotatory strength which result from interactions of the 1La transitions of the active-site tryptophans with the acetamide groups of the inhibitor. The reasonable agreement which is found between the experimental and calculated rotatory strengths implies that the crystal conformation of lysozyme must resemble the solution conformation.
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  • 69
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of the following oligo- and co-oligopeptides by the liquid-phase method is described: (L-Met)15 (I), [L-Glu(OBzl)]20 (II), (L-Val)8-Gly (IV), (L-Ile)8-Gly (V), (L-Ile)4-Gly-(L-Ile)4 (VI), (L-Ile)4-Pro-(L-Ile)4 (VII), (L-Met)5-L-Pro-(L-Met)5 (VIII), [L-Glu(OBzl)]7-L-Pro-[L-Glu(OBzl)]7 (IX). The oligomers are covalently bound to bifunctional polyethylene glycol (PEG) and monofunctional PEG-M of Mr 5 × 103-2 × 104. Analytical controls were carried out after each step of synthesis in order to ensure quantitative coupling yields. All products could be obtained in high purity as indicated by amino acid analysis, thin-layer chromatography and chiroptical methods. The solubility of the oligomers was strongly enhanced by the presence of the C-terminal PEG group, enabling conformational investigations in a variety of solvents. A significant relationship between conformation and physicochemical properties of the oligopeptides was observed. Oligomers with tendencies to adopt α-helical (I, II) or unordered structures (VI-IX) showed no pronounced change in solubility or coupling kinetics during chain elongation, whereas the onset of a β-structure (IV, V) was paralleled by a drastic decrease in solubility and reactivity of the terminal amino groups. Most notably, the insertion of a proline or glycine in the middle of a β-forming peptide chain (VI, VII) resulted in a considerable increase in solubility compared to the corresponding homo-oligomers. The impact of the conformational properties of a peptide chain on strategic considerations of peptide synthesis in solution is delineated.
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  • 70
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational analysis of the CD spectrum is reported for the synthetic and membrane-modifying nonadecapeptide analog of alamethicin N-t-Boc-(Aib-L-Ala)5-Gly-Ala-Aib-Pro-Ala-Aib-Aib-Glu(OBzl)- Gln-OMe. The CD data are evaluated according to three different methods and are discussed with respect to those obtained from natural alamethicin and suitable models such as N-t-Boc-(Aib-L-Ala)7-OPOE, fragments of the synthetic nonadecapeptide, and the hexadecapeptide N-t-Boc-(Aib-L-Ala)5-Pro-Ala-Aib-Aib-Glu(OBzl)-Gln-OMe. The synthetic nonadecapeptide with the longer helical region exhibits membrane activities comparable to those of alamethicin, whereas the hexadecapeptide with the shorter helix is inactive.
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  • 71
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    Biopolymers 19 (1980) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 72
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    Biopolymers 19 (1980), S. 231-240 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper deals with the light scattering from particles rotating in a flow with a transverse velocity gradient. It is theoretically substantiated and experimentally proved that the scattered light spectrum contains reliable information of the particle configuration and dimensions. The proposed technique may prove also very promising for the analysis of particle polydispersion.
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  • 73
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of poly(ε-L-lysine) is described. This is a poly(ε-amino acid) in which the ε-amino group of lysine is condensed with the α-carboxyl group to produce a chain backbone that is a variant of the usual one seen in proteins and the side chain is the α-amino group. Conformational studies of poly(ε-L-lysine) and its t-butyloxycarbonyl derivative suggest the likelihood of a chain order that is formally similar to the antiparallel pleated-sheet conformation of proteins.
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  • 74
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied the kinetics of oscillatory tensile forces in collagen membranes. These forces were generated by sinusoidal electric fields applied across the membrane. Both the magnitude and phase of the measured force changed with frequency over a three-decade range. The membrane-separated electrolyte baths had different ionic strength but identical non-isoelectric pH. Changes in intramembrane ionic strength due to the electric field were calculated over the same frequency range via an electrodiffusion model that was generalized to include convection and electrokinetic coupling. A comparison of the experimental and theoretical phases and amplitudes versus frequency suggests that electrodiffusion is the dominant rate-limiting process in this electromechanochemical transduction. These results are relevant to electrostatic interactions in connective tissues and to membrane-based filtration devices in which membrane permeability may be actively varied and controlled by an applied electric field.
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  • 75
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    Biopolymers 19 (1980), S. 263-272 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Integral enthalpies of solution of several dipeptides and tripeptides in water at low concentrations have been determined at 25 and 35°C. These data have been used to derive the changes in heat capacity on dissolution at infinite dilution ΔCp0 at 30°C. Limiting partial molal heat capacities ΔCp20 have been determined by combining ΔCp0 with Cp2 (heat capacity of pure solid peptides). Using the data on ω-amino acids and these peptides, the partial molal heat capacity of a peptide group —CONH— was semiquantitatively estimated.
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    Biopolymers 19 (1980), S. 273-284 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Integral enthalpies of solution at low concentrations of several amino acids and peptides in 2 and 6M urea solutions have been determined at 25 and 35°C. These data have been used to derive the enthalpies of transfer (at 25 and 35°C) and heat capacities of transfer (at 30°C) of these amino acids and peptides from water to aqueous urea solutions. Furthermore, the enthalpies of transfer and heat capacities of transfer per CH2 group and per peptide group —CONH— have also been estimated. These results show that while the enthalpies and heat capacities of transfer per CH2 group are positive and negative, respectively, the reverse is true for —CONH— group. The implications of these results in the mechanism of the denaturation of proteins by urea are discussed.
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  • 77
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The CD spectra of cUpUp, cCpCp, and cGpGp derived from DCC-catalyzed polymerization of the relevant protected ribonucleoside 3′-phosphates are described. Similar studies on Up, U 〉 p, and cUp, as well as cUpUpUp and cUpUpUpUp, are presented. The spectral properties of the cyclic oligomers are compared with those of the corresponding linear oligomers with terminal 3′-phosphates so as to demonstrate that disruption of normal right-handed base stacking is considerable in these RNA loops.
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  • 78
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    Biopolymers 19 (1980), S. 297-309 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The polymerization of 1,2-anhydro-3,4,6-tri-O-benzyl-β-D-mannopyranose proceeds in the presence of Lewis acids, cationic coordination catalysts, and strong bases. Debenzylation of the products yields oligomeric saccharides or low polymers. Polymerization in toluene by means of potassium alkoxide complexed with crown ethers leads to essentially stereoregular (1 → 2)-α-D-mannopyranan. The original derivatives have been characterized by optical rotation, viscosity, molecular weight, gel permeation chromatography, and spectrometry. The free polysaccharides have been characterized by optical rotation, molecular weight, and 1H- and 13C-nmr spectrometry and compared to yeast mannan hydrolysate oligomers.
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  • 79
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH3+ prototype test probe with B-form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH3+-like ion interacting with (G-C)4, (A-T)4, and [(G-C)·(A-T)]2 deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH3+-like ion is near known alkylation sites. The results of the Az+ … [(G-C)·(A-T)]2 interaction are virtually identical to those found for the CH3+-like ion. Aqueous solvation energetics have little effect on the physical association of Az+ with [(G-C)·(A-T)]2.
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  • 80
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    Biopolymers 19 (1980), S. 325-340 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of molecular orbital calculations, using MINDO/3 and CNDO/2L methods, have been used to characterize the chemical reaction of protonated aziridine with DNA nucleophilic base sites. The N-7 atom of guanine is found to be the preferred alkylation site only when the O-6 atom of guanine is involved in base-pair hydrogen bonding. Otherwise O-6 is the predicted major site of alkylation. This indirectly suggests that protonated aziridine alkylation processes involve base-paired DNA structures, since N-7 guanine is the observed major site of alkylation. Alkylation of N-3 adenine is predicted to be more favorable than chemical attack of the N-7 adenine position. Both of these sites, however, are predicted to be less reactive than N-7 of guanine. These chemical reactivity studies resolve alkylation specifically not achieved in the DNA-alkylator physical association calculations reported in the preceding paper.
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  • 81
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    Biopolymers 19 (1980), S. 341-352 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Infrared dichroic studies and deuterium exchange measurements of somatostatin and some of its analogs incorporated in uniaxially oriented polyoxyethylene are described. Band positions and dichroic ratios in the N-H stretching and amide I and II regions are similar to those of flexible and nonordered peptides like valinomycin and poly[Glu(ONa)]. This information, together with fast deuterium exchange rates, suggests that somatostatin exists in a flexible nonordered conformation in polyoxyethylene. One analog, di-S3,14-acetamidomethyl dihydrosomatostatin, was found to exist in both nonordered and β-like conformations.
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  • 82
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    Biopolymers 19 (1980), S. 395-418 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Monte Carlo simulation of the structure of the 16 ordered and disordered waters in the unit cell of crystals of the cyclic peptide cyclo(-L-Ala-L-Pro-D-Phe)2 is reported. The water structure has been characterized in terms of the statistically averaged positions of the individual molecules, their root-mean-square movements about these positions, the probability of finding a water in a given spatial position in the crystal (probability maps), and examination of individual configurations of the system. In this way a picture is obtained of the water structure, including water orientations (hydrogen positions), the hydrogen-bonding network, and fluctuations in these structural features, to a degree hitherto unavailable either from experimental or theoretical studies. In addition, the variation in water structure in various peptide environments was studied and correlated with the energetics of the individual water molecules. Variations in the crystalline environment of different water molecules lead to energy differences of as much as 4-5 kcal/mol in their average energies. Similarly, differences are observed in the water-peptide and water-water components of the energy. Two different water potentials were tested. The results were compared with experimental data in terms of mean positions, root-mean-square movements, and the Fourier transform of the simulated water structure. The agreement factor (R factor) calculated from the theoretical water probability distribution was 18.8% compared to the x-ray value of 14.5%, and the value of 28% when the water is omitted.
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  • 83
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    Biopolymers 19 (1980) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 84
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    Biopolymers 19 (1980), S. 445-448 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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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: Conformational energy calculations on the N-acetyl-N′-methylamides of dehydroalanine and N-methyldehydroalanine indicate that their conformational behavior is very different from that of the corresponding saturated compounds. The conformational data in the literature from x-ray and nmr investigations on peptides containing α,β-unsaturated residues are discussed on the basis of these theoretical results.
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  • 86
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    Biopolymers 19 (1980), S. 493-507 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amphipatic block copolymers (OβEb) with a hydrophilic saccharide block and a hydrophobic polypeptide block were synthesized. In these copolymers the saccharide block is the glyco-amino acid Oβ from ovomucoid and the peptide block (Eb) is a poly(γ-benzyl-L-glutamate) block. Copolymers OβEb exhibit, in the solid state and in Me2SO concentrated solutions, mesomorphic lamellar structures where the polypeptide chains are in an α-helical conformation. Depending on the molecular weight of the polypeptide block, three types of lamellar structures are obtained, and they differ by the mode of organization of the polypeptide chains in their lamellae and by the T or Y conformation of the saccharide block.
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  • 87
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formation of complex between the Cu2+ ion and poly(α-L-glutamic acid) [poly(Glu)] in 150 mM NaCl solutions was studied by uv-visible absorption and equilibrium dialysis methods at the mixing ratios of Glu residues to Cu2+, R, of 32, 16, and 8 and in the pH range 4-7. The results showed that more than 90% of Cu2+ ions bind to the poly(Glu) at pH 〉 4.9, but the bound Cu(II) begins to dissociate with a decrease in pH. The absorption spectra of bound Cu(II) varied with pH and R in a complicated manner. Three different component spectra were disclosed from the analysis of the pH dependence of the bound spectra. We concluded that poly(Glu)-Cu(II) complexes fall into three classes in the pH range 4-7, with the proportions of these complexes varying with both pH and R. The three complexes predominate either in the helix or extended-coil region, in the helix-coil transition region, or in the helix-aggregate region. The stability constant and binding mode of each Cu(II)-Glu complex were estimated from the dialysis data. With these results, the possible structure of each complex is discussed.
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  • 88
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The variable-temperature proton nmr spectra of the oligoribonucleotides in the series CpApX and the series ApGpX, X = A, G, C, U, together with the parent dimers CpA and ApG have been measured. A complete analysis of all the nonexchangeable base proton resonances and ribose H-1′ proton resonances was made. The presence of trends in the shielding abilities of the various bases at both the nearest-neighbor and next-nearest-neighbor positions were identified. The observed shieldings could be used to predict the chemical shifts of protons in related systems. Based on the empirical results from ribodinucleoside monophosphates, the temperature-dependent behavior of the J1′2′ coupling constants of the triribonucleotides suggested that the compounds in the CpApX series stacked from the 5′-end to the 3′-end, while those in the ApGpX series stacked from the 3′-end to the 5′-end.
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  • 89
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    Biopolymers 19 (1980), S. 619-637 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Closed random Gaussian polygonal chains of N (6 〈 N 〈 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types - 0, 31, 41, 51, and 52 - the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw2/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N1/4 (w/N)2, and therefore depends on the writhing density and on the length of the DNA.
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  • 90
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    Biopolymers 19 (1980), S. 575-595 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A band-centrifugation method for the analysis of an assembly reaction of a simple virus from its RNA and protein is described. The experiment was carried out by sedimenting a band of viral RNA through a solution of depolymerized coat protein. The resulting radial distribution of the reaction products, followed as a function of time, was analyzed by a computer simulation of the series of reaction. This method is based on a numerical solution of the continuity equation for the sedimentation-diffusion process [Claverie, J.-M., Dreux, H. & Cohen, R. (1975) Biopolymers 14, 1685-1700; Cohen, R. & Claverie, J.-M. (1975) Biopolymers 14, 1701-1716]. A numerical method for the simulation of the chemical reaction is derived. From the simulated reaction series, equilibrium constants emerge for the successive addition of protein subunits to the growing nucleoprotein particle.The method is applied to the assembly of alfalfa mosaic virus. If the reaction between RNA and protein is carried out in 0.32M CsCl, pH 7.0, two stages during particle growth are resolved, each characterized by an equilibrium constant K. The determined values for K range from 5 × 105 to 3 × 106 l. mol-1. The existence of these two stages may have a structural implication in the assembly, as they likely represent an elongation and a termination stage. If the reaction is carried out under more favorable conditions (0.25M CsCl, pH 7.0), a kinetic constant of at least 105 l. mol-1 sec-1 is derived for each reaction step. Under these conditions the assembly appears to be completed within 1 min, which is too fast to detect distinct stages by band sedimentation.
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  • 91
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    Biopolymers 19 (1980), S. 597-617 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Purified insoluble elastin samples labeled with [1-13C]valine, [1-13C]alanine, and [1-13C]-lysine were prepared from chick aorta in culture. The molecular mobility at the labeled sites was investigated using 13C-1H magnetic double-resonance spectroscopy. Linewidths, T1, and nuclear Overhauser effect (NOE) values of the labeled carbons alone were obtained from dipolar decoupled difference spectra. Analysis of these parameters together with signal intensity measurements showed that essentially all the valyl residues, ca. 75% of the alanyl residues, and ca. 60% of the lysyl residues were characterized by rapid backbone motions having τ = 65 nsec. Resonances due to the remaining alanyl and lysyl residues were detected in cross-polarization experiments, which enhance the signals of motionally restricted carbons. Since lysyl and alanyl residues are found in the crosslink regions of elastin, whereas valyl residues are not, we conclude that crosslinks rather than secondary structures in the extensible region of the protein are the main source of motional restrictions in the protein. Elastin chain mobility was monitored by linewidth measurements over the range -90 to +70°C. When the swelling solvent (0.15M NaCl) was fixed at 0.6 g/g of elastin, a rapid monotonic reduction in chain mobility was observed as the temperature was lowered from 50 to 5°C. Liquidlike mobility was completely lost at 5°C. In contrast, the same sample in contact with excess solvent retained its liquidlike molecular mobility until -13°C, where it abruptly became rigid. The molecular mobility of this sample was temperature insensitive in the physiologically interesting range, 20-40°C, as a consequence of the opposing influences of temperature and swelling. Taken together these nmr data indicate that under physiological conditions, elastin is a network of mobile chains whose motions are strongly influenced by protein-solvent interactions.
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  • 92
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    Biopolymers 19 (1980), S. 639-653 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preferential solvation of the glucans amylose, pullulan, and dextran in binary dimethyl-sulfoxide/water (DMSO/H2O) solvent mixtures has been measured using gel-permeation chromatography. The preferential solvation behavior of the three glucans in DMSO/H2O solvent mixtures is indistinguishable in the experiments reported. In solvent mixtures with mol ratio DMSO/H2O less than 1:2, all three glucans are solvated preferentially by H2O. The maximum extent of preferential solvation by H2O is about 2.5 mol H2O/mol of glucose residues. When the DMSO/H2O mol ratio exceeds 1:2, DMSO solvates the glucans preferentially to a maximum extent of about 1 mol DMSO/mol of glucose residues. An interpretation of the change in preferential solvation with mixed solvent composition is suggested in terms of the known characteristics of the binary solvent system, and the relationship of preferential solvation, reported here, to the absolute solvation of the glucan chains is discussed.
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  • 93
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    Biopolymers 19 (1980), S. 669-679 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dc electrical conductivity of large single crystals of hen egg-white lysozyme has been measured. The samples were grown from aqueous solution and dried in air with silica gel. The temperature dependence of the conductivity obeyed the relation σ = σ0 exp(- ΔE/kT), with ΔE = 1.2 eV. The ΔE value agreed with most of the previous results for various proteins in the form of lyophilized powder. On the other hand, log σ0, being between 7 and 11, was much larger than the previously reported values and differed among the samples. An irreversible decrease in σ0, without affecting ΔE, was observed on heating the samples above 85°C. It was shown that the set of results can be explained if the charge carriers responsible for the observed conduction are regarded as protons, originating from residual water molecules. Photoresponse of the samples to uv radiation below 305-315 nm was also observed. Reproducible and reliable results were obtained relatively easily in the present experiments, which is thought to be the main advantage of using single-crystalline samples.
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  • 94
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    Biopolymers 19 (1980), S. 751-766 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general formalism, which includes translation-rotation coupling, is proposed for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape. This formalism is based on Brenner's theory of translational-rotational dynamics and on methods for the calculation of hydrodynamic properties that have been already presented, and can be regarded as a generalization of the one proposed by Nakajima and Wada. The calculated transport properties depend on the origin as predicted by Brenner's theory, but in a disagreement with him, the center of resistance and the center of diffusion do not coincide. As one can define several hydrodynamic centers, which in practice turn out to be located at different points, the influence of the choice of the center on the calculated transport properties is discussed. An analysis of the translation-rotation coupling effects in translational diffusion reveals that they arise exclusively from hydrodynamic interactions and are rather small in some cases of interest. Finally, we present a study of the rotational diffusion of rigid bent rods with a fixed length-to-diameter ratio. The diffusion coefficients obtained can be useful to estimate changes with respect to a straight rod.
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  • 95
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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  • 96
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 6 (1972), S. 154-161 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 6 (1972), S. 162-163 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 6 (1972), S. 164-164 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 6 (1972), S. 167-174 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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