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  • Polymer and Materials Science  (2,332)
  • General Chemistry  (1,021)
  • COMMUNICATIONS  (315)
  • Cell & Developmental Biology
  • 1980-1984
  • 1970-1974  (3,855)
  • 1972  (3,855)
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  • 1980-1984
  • 1970-1974  (3,855)
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  • 1
    Electronic Resource
    Electronic Resource
    Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond modelFrom the thesis submitted by Wilma K. Olson in fulfillment of the requirements for the degree of Doctor of Philosophy, Stanford University, 1971. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1-23 
    Details
    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.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110102
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  • 2
    Electronic Resource
    Electronic Resource
    Isoenzymes of tetrameric proteins (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 119-126 
    Details
    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.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110109
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  • 3
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    Graphical approach to non-ideal cases of self-associating protein systems (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 197-214 
    Details
    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.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110115
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  • 4
    Electronic Resource
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    Fibrillar aggregates of poly-γ-benzyl-L-glutamate (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 271-278 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110120
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  • 5
    Electronic Resource
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    Lysine oligopeptides. Preparation by ion-exchange chromatographyOn leave from the Department of Biophysics, The Weizmann Institute of Science, Rehovot, Israel. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 607-621 
    Details
    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.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110306
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  • 6
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    Independence of length and temperature effects on the rate of helix formation between complementary ribopolymers (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 549-561 
    Details
    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.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110303
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  • 7
    Electronic Resource
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    Evidence for stereospecific collision complexes of cyclo(tri-L-prolyl) with benzene (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 653-659 
    Details
    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.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110310
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  • 8
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    Thermal denaturation of nucleohistones - effects of formaldehyde reaction (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 835-847 
    Details
    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.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110408
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  • 9
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    Linear relaxation analysis of the mechanochemical transformation of collagen fibers (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 899-912 
    Details
    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.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110413
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  • 10
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    Thermodynamic analysis of thermal transitions in globular proteins. I. Calorimetric study of ribotrypsinogen, ribonuclease, and myoglobin (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 935-935 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110415
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  • 11
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    On the application of polyelectrolyte “limiting laws” to the helix-coil transition of DNA. I. Excess univalent cations (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 937-949 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110502
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  • 12
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    The conformation fo poly-L-alanine in hexafluoroisopropanol (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1001-1020 
    Details
    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.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110506
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  • 13
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    PPP calculations of the circular dichroism spectra of some dinucleoside phosphates (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1091-1102 
    Details
    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.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110511
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  • 14
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    Synthesis and conformational study of poly(N∊-benzyl-L-lysine) and its benzyloxycarbonyl derivative (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1259-1268 
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    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.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110610
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  • 15
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    Detection of polar side-chain hydration in polypeptides by near-infrared spectroscopy (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1305-1310 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110614
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  • 16
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    Simple sequential model for the kinetics of conformational transitions of oligomeric helices and proteins (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1499-1520 
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    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.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110713
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  • 17
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    Masthead (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110801
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  • 18
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    Far-infrared spectra of sequential copolymers of amino acids with alkyl group side chains (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1593-1605 
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    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.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110806
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  • 19
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    Induced cotton effects of tRNA-acridine orange complex and tRNA conformation (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1583-1592 
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    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.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110805
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  • 20
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    The hydrolysis of poly (L-prolyl-glycyl-L-prolyl) by bacterial collagenase (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1607-1612 
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    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.
    Additional Material: 1 Tab.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110807
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  • 21
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    Effect of non-complementary nucleotides on the rate of helix formation: Kinetics of formation of poly (I)·poly (C,I) and poly (I)·poly (C,U) complexes (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1613-1620 
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    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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    URL: http://dx.doi.org/10.1002/bip.1972.360110808
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    The kinetics of the renaturation of deoxyribonucleic acid denatured in the presence of copper (II) ions (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1661-1684 
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    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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    Conformational studies on copolymers of L-leusine and L-leucine: Circular dichroism and potentiometric titration studies (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1723-1744 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    The absence of an isotope effect on the stability of the poly-β-benzyl-L-aspartate α-helix in aprotic solvents (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1745-1763 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Conformational aspects of polypeptide structure. XLI. Crystal structure of S-thiazolidine-4-carboxylic acid and helical structure of poly[(S)-thiazolidine-4-carboxylic acid]This work was carried out at the Polytechnic Institute of Brooklyn and the Istituto Chimico, Naples, Italy. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1779-1787 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Optical rotatory dispersion and circular dichroism of benzoyl polysaccharidesParts of this work were presented at the “Makromolekulare Kolloquium” 1969, Freiburg/Brsg., BRD. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1997-2013 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Spectroscopic study of monosubstituted amides. II. Rotation isomers in amides substituted by aliphatic side-chain modelsFor Part I See Ref. 3. This paper is one part of F. Fillaux's thesis registered by the CNRS (France) under No. A07245. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2063-2077 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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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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    Viscosity of heparin as a function of dielectric constant and of desulfation (1972)
    New York : Wiley-Blackwell
    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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    New banding species, with densities of phage-ghost clusters, produced from lambda phage particles on storage (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2171-2177 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Synthetic peptides related to the entire sequence of yeast iso-1-cytochrome C (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2191-2194 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    A comparative X-ray study of a nucleoprotamine and DNA complexes with polylysine and polyarginine (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2223-2231 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    The pH dependence of tyrosine cyanuration in proteins (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2233-2240 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Salt bonding in proteins. A model for the abnormal hydrogen ion titration and the strong anion binding of serum albumin (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2197-2221 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    The β-conformation and association of low-molecular-weight poly-γ-benzyl-L-glutamate in Solutions (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 493-507 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Perspectives report: Melting of DNA. Its study and application as a research method (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 527-528 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Dielectric dispersion of the α-helix at the transition region to random coil (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 587-605 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    Conformational studies on polypeptides. The effect of sodium perchlorate on the conformation of poly-L-lysine and of random copolymers of L-lysine and L-phenylalanine in aqueous solution (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 633-643 
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    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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    Pressure dependence of the helix-coil transition temperature for polynucleic acid helices (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 667-678 
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    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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    The molecular weight of a fast sedimenting MS2 RNA form (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 735-735 
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    The helix-coil transitions of poly (dA). Poly (dT) and poly (dA-dT). Poly (dA-dT) (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 745-759 
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    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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    The ultraviolet circular dichroism of some natural DNAs and an analysis of the spectra for sequence information (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 853-879 
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    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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    Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotidesFrom the thesis submitted by Wilma K. Olson in fulfillment of the requirements for the degree of Doctor of Philosophy, Stanford University, 1971. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 25-56 
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    Notes: Conformational energies are calculated for pairs of successive bond rotations within an internal residue of a polyribonucleotide chain. Contributions to these energies include bond torsional strain, van der Waals repulsions, London attractions, electrostatic interactions, and inductive interactions between nonbonded atoms in the nucleotide repeat unit. The average dimensions of unperturbed random-coil polyribonucleotide chains are then evaluated on the basis of energies thus estimated, using for this purpose the previously developed virtual bond treatment. The characteristic ratio \documentclass{article}\pagestyle{empty}\begin{document}$ C_\infty = \mathop {{\rm lim}}\limits_{n \to \infty } (\langle r^2 \rangle_0/nl^2) $\end{document} of the mean-square end-to-end distance calculated for polyribonucleotide chains in which all pentose rings are fixed in a C3′-endo conformation is ≈9; for chains consisting exclusively of C2′-endo units it is ≈25. These values are considerably greater than those obtained by giving equal weight to all conformations judged to be sterically allowed. Satisfactory agreement between the calculations here and experimental values from viscosity and light-scattering studies is achieved by treating the chain as a random copolymer of C3′-endo and C2′-endo conformational isomers. The critical dependence of the characteristic ratio on the rotation about bond C3′-O3′ in the C2′-endo chain, however, obscures the interpretation of chain dimensions. The chain is also treated in higher approximation as a sequence of independent repeat units, each of which consists of six chemical bonds. The characteristic ratio obtained in this manner is 6.5 for the C3′-endo chain and 18.5 for the C2′-endo chain. Finally, the effects of partially stacked conformations in polyribonucleotides are investigated using the virtual bond treatment. Chain dimensions are calculated for random coil poly rA chains in which stacking is introduced by both noncooperative and cooperative processes.
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    On hydrogen bonding in amylose (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 315-318 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Far ultraviolet optical activity of saccharide derivatives. I. Xylan and cellulose acetates (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 291-301 
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    Notes: Optial rotatory dispersion (ORD) and Circular dichroism (CD) spectra of several β-1,4 xylan and cellulose acetates and some of their oligomers were investigated. The CD spectra proved considerably superior in terms of information content and interpretability. Comparison of the xylan and cellulose acetate series which also included partially substited cellulose acetates showed that the sign of the CD of the C(6) acetyl was negative. Likewise, the combined contribution of C(1) and C(4) to their equatorially substituted acetyls was positive (with C(1) definitely Positive) and the combined contribution of C(2)eq and C(3)eq negative. The solution conformations of both polysaccharide acetates appeared to be random. The CD of White birch xylan acetate which is substituted on the average at every tenth residue with a 4-O-methyl glucuronic acid substituent, was sensitive to it. The xylan oligomer series also illustrated that CD may be used to determine the degree of polymerization of these oligomers up to about 20.
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    Dielectric properties of polyelectrolytes. II. A theory of dielectric increment due to ion fluctuation by a matrix method (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 347-359 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The mean square of dipole moment of a linear macromolecule which is responsible for dielectric increment of aqueous polyelectrolyte solutions is calculated by means of a matrix method in which ion binding at discrete sites and the nearest-neighbor interaction are taken into account. On the basis of the relationship between polarization of poly-ion and fluctuation of bound counterions the present theory indicates that the loosely bound ions result in larger increment and otherwise smaller increment. Also, the theory predicts that the dielectric increment has a maximum at an intermediate monovalent-divalent ion ratio when both species coexist. These results are consistent with experiments on polyacrylic acid neutralized with NaOH and Ca(OH)2. At large contents of divalent ions the effect of chelation is also discussed.
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    Nuclear magnetic resonance spectra of poly(N-alkylamino acid)s (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 399-408 
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    Notes: 220-MHz NMR spectra of various poly (N-alkylamino acid)s are investigated. Spectra of polysarcosine recorded in various solvents showed fine splittings of the methyl and methylene bands. Comparing the spectrum with that of its model compound, the fine structure of the methyl band of polysarcosine was assigned to four dyad sequences of the cis-trans isomeric state of the main chain amide bonds. Also the methylene band was roughly divided into cis and trans bands. From the temperature dependence of the spectra of polysarcosine, a double coalescence phenomenon was observed, in which the four dyad peaks coalesced into two peaks corresponding to cis and trans, then the two peaks coalesced into one peak. Further, the approximate value of the free energy for the internal rotation of the main chain amide bond was estimated. NMR spectra of various poly(N-alkylglycine)s in methylene chloride solution were also obtained. From the comparsion of their methylene bands, the introduction of the bulky N-alkyl groups was found to increase the cis content of the amide bond.
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    Physico-chemical description of a condensed form of DNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 443-459 
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    Notes: When exposed to a low pH, in various ionic strength conditions and in sufficiently dilute solutions, DNA undergoes a transition, revealed by an increase in optical density. A careful analysis shows that, associated with this transition, there is an effective decrease in absorbance, overcompensated by an increase in scattering. The conditions for the new transition can be summarized conveniently by a graph in a pH-Na+ molarity diagram. If the pH of a DNA solution is progressively lowered at constant Na+ concentration, one finds first the melting transition (I), and at lower pH values, the new transition (II). If the same experiment is performed on pre-denatured DNA, only transition II will be found. If native DNA is brought directly to the low pH conditions, without allowing it to denature irreversibly at intermediate pH values, transition II is reversible (with a small hysteresis effect). DNA, initially native, neutralized after prolonged exposures to the low pH, recovers the buoyant density value of native DNA, along with the absorption and scattering properties of the native state. The experiments are consistent with the interpretation that a new state exists in which DNA, still double stranded, assumes a very compact shape (of the order of 1500 Å in diameter for T2 DNA), with a hyperchromicity value of 10-14% above the native value. Nearly monodisperse suspensions of DNA molecule in this apparent state may be obtained only at very low concentrations (∼0.25 μg/ml). At 1 μg DNA/ml aggregation is noticeable. The possible connection with the condition of intraphage DNA is discussed.
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    Macromolecule-small molecule interactions; introduction of additional binding sites in polyethyleneimine by disulfide cross-linkages (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 483-491 
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    Notes: Polyethyleneimine and its acyl derivatives have been thiolated with thiobutyrolactone and the SH groups introduced have been crosslinked in the presence of and in the absence of methyl orange, respectively. After crosslinking of the polymers, the bound methyl orange was removed. The resultant two kinds of crosslinked polymers have been examined for their ability to bind methyl orange. The polymer crosslinked in the presence of methyl orange shows more binding sites and stronger binding than does the polymer crosslinked in the absence of methyl orange. It seems, therefore, that the conformation of the polymer may be molded to provide sites that can accommodate a specific small molecule.
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    Masthead (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    URL: http://dx.doi.org/10.1002/bip.1972.360110301
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    Synthesis and conformations of periodic copolypeptides of L-alanine and glycine (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 563-586 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Additional Material: 5 Ill.
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    Electric birefringence and dichroism of acridine orange and methylene blue complexes with polynucleotides (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 645-652 
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    Notes: Electro-optic measurements are reported for the polynucleotides poly A, poly U, poly G, and NaDNA, and their complexes with acridine orange (AO). Measurements were also made on the methylene blue (MB) complex with NaDNA. Poly U, poly G, and NaDNA complexes with AO as well as the NaDNA-MB complex were found to exhibit positive birefringence and perpendicular dichroism indicating the dye molecules are oriented with their long axes perpendicular to the applied electric field. The opposite was found for the AO complex with poly A, which showed positive birefringence and parallel dichroism, indicating that in this case the dye molecules are oriented with their long axes parallel to the field.
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    Small-angle x-ray scattering by poly-L-alanine solutions (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 679-682 
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    Notes: The radius of gyration and “persistence length” of poly-L-alanine, calculated from small-angle x-ray scattering data, have values of 56 Å and 44 Å, respectively, in dichloroacetic acid, and 78 Å and ∼30 Å in a 1:1 v/v mixture of trifluoroacetic acid and trifluoroethanol. This can be interpreted to mean that poly-L-alanine exists in a relatively rigid, predominantly α-helical conformation in dichloroacetic acid and in an extended, more flexible form in the mixed solvent system.
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    Circular dichroism of DNA: Temperature and salt dependence (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 761-779 
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    Notes: The temperature dependence of the circular dichroism and ultraviolet absorbance of calf thymus DNA and poly dAT were measured in aqueous solutions of various 1-1 electrolytes. Although there was very little change in absorbance, the circular dichroism changed dramatically as a function of both temperature and solvent. There is a correlation of the heat of hydration of the cation and the magnitude of the temperature dependence of the circular dichroism. Our results are interpreted in terms of a large number (possibly a continuum) of intermediate secondary structures.
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    The crystal structure of amylose-DMSO complex (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 849-852 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Additional Material: 1 Ill.
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    Anisotropic scattering by single starch granules. II. Layered granule structureReference 1 is the first part of this series. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 881-892 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The study of anisotropy light scattering from tapioca and potato starches has continued with the recording of more detailed experimental single-granule Hv scattering patterns and, for the first time, single-granule Vv patterns. Quantitative analysis of the higher order scattering maxima to the granule morphology, permitting an analysis of the latter in terms of a lyered structure. For tapioca starch, this analysis indicates that if layering is present at all, the layer thickness is comparable to the wavelength of the incident radiation, and most likely is considerably less than 0.5 μ in thickness. On the other hand, the potato starch morphology is characterized by a relatively coarse layering with few layers and considerable difference in the anisotropy between successive layers. The models for the two starches in best agreement with experimental data are as follows: almost perfectly spherulitic anisotropic structure with very thin shell-like layers - if any - for tapioca, and alternating layers of varying anisotropy several microns in thickness and probably simultaneously present with an isotropic center, for potato starch. The Vv pattern for tapioca starch is in agreement with this model, although its information content is lower owing to the experimental difficulty of recording higher order maxima. Suggestions for further morphological study of starches are presented.
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    On the Application of Polyelectrolyte “Limiting Laws” to the Helix-Coil Transition of DNA. II. The Effect of Mg++ Counterions (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 951-955 
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    Notes: The techniques of the previous article are here applied to the case for which the solution contains, in addition to excess uni-univalent salt, one equivalent of divalent counterions per mole nucleotide. In agreement with the melting temperature measurements of Dove and Davidson for Mg++, it is predicted that a region of uni-univalent salt concentration then exists in which (dT m/d log m A+) is negative. It is further predicted, in accord with experiment, that in the presence of divalent counterions, the helical form of DNA is much more stable than in their absence.
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    The determination of the thermodynamic parameter of the helix-coil transition of polypeptides by means of dipole moment measurements (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1021-1030 
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    Notes: The theoretical change of the mean-square dipole moment of a polypeptide during the helix-coil transition is compared with the change in helix content. It is shown that, according to the theory, the determination of the helix initiation parameter σ and the enthalpy of helix formation ΔH can be determined. Experimental data on poly-benzyl-L-gluatamate in two different solvent mixtures are given.
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    Optical properties and base pairing of E. coil 5S RNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1031-1039 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The ultraviolet absorption, optical rotatory dispersion, circular dichroism, and infrared absorption spectra of renatured 5S RNA have been measured at pH 7.0 in 0.1M NaCl at 25° and used to obtain four independent estimates of the number of base pairs. These four estimations are in reaonable agreement and average values of 28 ± 4 G.C and 13 ± 4 A.U. base pairs.
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    Matching of single-strand breaks to form double-strand breaks in DNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1116-1116 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Far-infrared spectra of copoly(-α-amino acids) (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1137-1148 
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    Notes: Far-infrared spectra in the region from 700 to 200 cm-1 were measured for the copolymers of L-alanine and glycine, those of L-alanine and L-valine, those of L-alanine and L-leucine, and those of L-alanine and L-phenylalanine. The observed spectra were interpreted on the basis of the analysis of the far-infrared spectra of the corresponding homopolymers, and the correlation between the conformations of the copolymers and the kinds of the component amino acids was discussed.
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    The circular dichroism of aromatic polypeptides: Theoretical studies of poly-L-phenylalanine and some para-substituted derivatives (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1149-1171 
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    Notes: We have calculated rotational strengths and circular dichroism (CD) curves for sidechain and backbone transitions in poly-L-Phenylalanine (PLP), POLY-p-amino-L-phenylalanine (PPALP), poly-p-chloro-L-phenylalanine (PPCLP), poly-o-acetyl-L-tyrosine (POALT), and poly-p-nitro-L-phenylanine (PPNLP), using methods applied previously to poly-L-tyrosine (PLT). Comparison of the theoretical CD curves with available experimental data for PLP and PPALP indicate that these polypeptides form right-handed helices with side-chain conformations similar to that of PLT. For PPNLP, where experimental data are also available, no conformational assignment could be made, as none of the calculated curves gave good agreement with experiment. Possible reasons for this lack of agreement are discussed. For the other two polypeptides, PPCLP and POALT, although no experimental data are yet available, the calculated curves indicate that an unambiguous assignment should be possible. For the conformations (RA and LA) in which the side chains are packed more loosely, there are strong similarities in the calculated CD curves of a particular conformation, regardless of the para substituent. In the tighter R1 and L1 conformations, few generalizations can be drawn, each derivative having a distinctive pattern. In PLP, PPCLP, and POALT, where the side-chain La band is in the 200-210 nm region, the L1 conformation exhibits a negative nπ* rotational strength, opposite to that expected for a left-handed helix. One must therefore be cautious about assigning the helix sense of aromatic polypeptides on the basis of the sign of the nπ* CD band. Side-chain nπ* transitions present in POALT and PPNLP were found to have small rotational strength.
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    Conformational studies of α-glucansContribution No. 345 from the Centre of Advanced Study in Physics, University of Madras, Madras, India. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1379-1394 
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    Notes: A study of the effect of linkage on the possible conformations of di-and polysaccharides of α-D-glucose and also the probable intramolecular hydrogen bonds has been made. The differences in the nature of linkage is shown to effect the energetically preferred conformations; (1 → 2) linkages lead only to righthanded helical conformations, (1 → 3) linkages lead to extended as well as both left and righthanded helical conformations; (1 → 4) linkages lead to both right-and lefthanded wide helical conformations. The possible hydrogen bonds between adjacent residues are also dependent on the nature of the linkage. A comparison of the conformational data of α-D-glucans with those of β-D-glucans has indicated that the favored conformations and hydrogen bonds between contiguous residues in the chain are influenced by the configuration at the anomeric carbon atom in all the three types of polysaccharides. From the energy calculations a probable conformation (φM = -10°, ψM = -30°, φN = -23°, ψN = -19°) has also been proposed for crystalline mycodextran in conformity with x-ray data. This conformation contains two types of hydrogen bonds between contiguous residues one between 0-2 and 0-3 atoms at (1 → 4) linkage and the other between 0-2 and 0-4 atoms at (1 → 3) linkage in the chain. The conformation of maltose unit (-10°,-30°) that is likely to occur in the crystalline mycodextran coincides with the minimum energy conformation of maltose.
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    Cooperative nonenzymic base recognition - a study of interaction of oligoguanylic acid with poly C (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1395-1410 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The interaction between poly C and (Gp)nG(n = 1,2) in dilute solution was investigated spectrophotometrically in 0.1M phosphate buffer pH 7.2 under conditions unfavorable for the formation of self-associated complexes of oligoguanylic acids. Two isosbestic points were observed when poly C was titrated gradually with GpGpG, one at 232-233 mμ(in the range of 0-33% poly C) and one around 238 mμ (in the range of 50-100% poly C). The melting temperature (Tm) of the 1:1 poly C: (Gp)nG complexes (n = 1,2) of varying concentration were determined. The equilibrium properties of the 1:1 complexes can be described by two interaction parameters, namely, (i) cooperative stacking interaction between the first nearest neighbor of the adsorbed oligomer, and (ii) intrinsic association constant of the adsorbed oligomer with its polymeric site, since the cooperative helix-coil transition particularly in the smaller oligonucleotide can be described by an “all or none” model. Based on such a model the enthalpy of stacking inteaction-dependent Tm values yielded directly the sum of the enthalpy of stacking interaction and of basepairing (which is dependent on the chain length of the oligomer) and the value of S, the stability constant of a G-C pair within a helix. The enthalpy of formation of G-C pair is then calculated as -6.3 kcal/base pair either from the chain length dependent enthalpy term or from the temperature coefficient of S values. From the S value and the association constant of 1:1 GpGpGpC:GpCpCpC complex, other thermodynamic parameters such as nucleation parameter (β) and free energy of stacking interaction can be obtained.
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    tRNA structure and binding sites for cations (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1317-1333 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Equilibrium dialysis and electronic and nuclear resonance spectroscopy show that tRNA cooperatively binds divalent metal ions at very low concentrations (free metal concentration 3 × 10 -6 M). The first two methods show that different purified tRNAs have a very similar behavior, including initiator tRNAFmet. tRNAs with an extra arm in the clover-leaf model, however, appear to have a slightly different behavior.The binding can be described in terms of two classes of sites. The cooperative association of divalent ions binding first does not parallel a cooperative change in the hyperchromism of the tRNA, while the non-cooperative association of the second class of divalent ions corresponds to the concentrations needed to obtain a cooperative melting of the tRNA.The temperature dependence of the number of binding sites and of their binding constants is also presented.The nature of the divalent ion gives the following efficiency: for the cooperativity Co++〉Mg++〉Mn++ for the weak binding sites Mn++〉Co++〉Mg++
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    Structure of β,D(1-〉4′)-xylan hydrate (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1335-1344 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A structure is proposed for xylan hydrate as a result of investigations by x-ray fiber diffraction and computer-aided chain-packing methods. The unit-cell dimensions are a = b = 9.16 Å, c (fiber axis) = 14.85Å, γ = 120° and the proposed anti-parallel chain arrangement corresponds to a space group symmetry of P3221. Left-handed threefold screw helices are stabilized in this conformation by their interaction with chains of water molecules, so that a satisfactory hydrogen-bonding scheme is achieved. The proposed structure provides an explanation of the changes in the x-ray diagram with relative humidity and yields a very good structure factors agreement. An x-ray fiber diagram corresponding to a higher hydrate (xylan dihydrate) is presented. Comments are made on the possible role of xylan in nature and in technological processes.
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    Studies on spin-labeled polyriboadenylic acid (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1421-1433 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Spin-labeled samples of poly rA, poly rU, and poly rG have been prepared, and physicochemical properties primarily of labeled poly rA are reported. The nitroxide radical, 4-(2-iodoacetamido)-2,2,6,6-tetramethylpiperidinooxyl, is incorporated to a greater extent in poly rA and poly rU, as compared to poly rG. No incorporation is observed in the case of poly rC. Special attention has been paid to the separation of the covalently attached labels from the free labels, and to the preservation of the integrity of the chain length of the labeled polymers. The determination of molar extinction coefficients of the three labeled polymers indicates virtually no difference from those known for the chemically unpertubed polyribonucleotides. The correlation times for the spin-labeled single stranded poly rA and poly rU have been calculated. More mobile building blocks are found in poly rU as compared to poly rA. Conformational properties of labeled poly rA in aqueous solutions have been investigated using electron spin resonance, circular dichroism, and absorption spectroscopy. The objective of the study of labeled poly rA was to examine its conformational transitions upon the uptake of protons by the adenine bases. Based on electron spin resonance data there is strong evidence that the single strand-double strand transition can take place in three steps. In addition to the already known two forms of double-stranded poly rA in acidic solution, called A and B, it is suggested that a third phase, consisting possibly of large aggregates, is involved in the transition of the less protonated double strands to those of complete protonation.
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    “Increased-valence” formulas for the iron-ligand bonding of some ferrohaemoglobin compounds (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1551-1565 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Valence formulas are constructed for the iron-ligand groups of the oxy-, carboxy-, nitric oxide-, and nitrosobenzene derivatives of haemoglobin. To do this, the newly developed “increased-valence” theory3 is used. The most stable of these valence formulae are able to account simply for certain iron-ligand properties, with the iron remaining essentially as ferrous, as it is in haemoglobin.
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    Study of the interaction of polynucleotide chains with oligomers by means of chromatography (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1541-1550 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method of measurement of the binding constant of oligonucleotides with complementary polynucleotide chains was developed using a gel filtration procedure. Data for complexing of poly U with triplets ApApA are presented and analyzed by means of a simple statistical theory of cooperative adsorption deduced by the Bethe-Guggenheim method. The complexes are triple, they contain two polymer chains bound by oligomers. The energy of stacking is found equal to 1300 cal/mol in fair agreement with earlier data of Ts'o. The energy of binding of a single triplet to both complementary chains is equal to 14,000 cal/mol.
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    Dielectric properties of polyelectrolytes. III. Effect of divalent cations on dielectric increment of polyacids (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1567-1582 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dielectric dispersion of polyacrylic acid (PAA) and polystyrene sulfonic acid (PSS) was measured in the presence of divalent cations. Effects of divalent ions were studied by neutralization with varying ratios of sodium hydroxide and divalent base concentration, addition of salts of divalent cations, and neutralization with divalent bases only. Two dispersion regions were observed in all cases, i.e., low-frequency dispersion (102-104 Hz) and high-frequency dispersion (105-106 Hz). The dielectric increment increases in the presence of sodium and alkaline earth metal ions together, but not with sodium and transition metal ions. This is due to the increment of low-frequency dispersion and is attributable to the fluctuation of bound counterions which is explained by our theory previously reported.1 In the case of PAA neutralized with large fractions of divalent ions, or with divalent ions only, the increment is very small because of reduction of the fluctuation by interaction between bound ions at the neighboring sites and reduction of the effective length of polyion probably due to chelation by divalent ions. There are some differences among the effects of Mg++, Ca++, and Ba++ on dielectric increment which may result from affinity or chelating ability of these ions.
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    Masthead (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.1972.360110901
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    Normal vibrations of polyglycine II (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1841-1853 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A valence force field has been refined for single-chain polyglycine II using the known structure and four isotopic derivatives. The calculated frequencies are in good agreement with the observed. The force field is compared with that derived from polyglycine I and for the nylons.
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    The conformation of polycytidylic acid, polyguanylic acid, polyinosinic acid, and their helical complexes in aqueous solution from laser Raman scattering (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1855-1869 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Raman spectra of the double helical complexes of poly C-poly G and poly I-poly C at neutral pH are presented and compared with the spectra of the constituent homopolymers.When a completely double-helical structure is formed in solution a strong sharp band at 810-814 cm-1 appears which has previously been shown to be due to the A-type conformation of the sugar-phosphate backbone chain. By taking the ratio of the intensity of the 810-814 cm-1 band to the intensity of the 1090-1100 cm-1 phosphate vibration, one can obtain an estimate of the fraction of the backbone chain in the A-type conformation for both double-stranded helices and self-stacked single chains. This type of information can apparently only be obtained by Raman spectroscopy.In addition, other significant changes in Raman intensities and frequencies have been observed and tabulated: (1) the Raman intensity of certain of the ring vibrations of guanine and hypoxanthine bases decrease as these bases become increasingly stacked (Raman hypochromism), (2) the Raman band at 1464 cm-1 in poly I is asigned to the amide II band of the cis-amide group of the hypoxanthine base. It shifts in frequency upon base pairing to 1484 cm-1, thus permitting the determination of the fraction of I-C pairs formed.
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    Ultrasonic absorption and relaxation spectra in aqueous bovine hemoglobin (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1973-1984 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of the frequency and pH dependence of acoustic absorption at 0°C in aqueous solutions of freshly prepared bovine oxyhemoglobin are reported. The role of ionization and possible direct proton-transfer between proximal pairs in determining the characteristic times for the relaxation of the internal charge distribution is discussed. It is concluded that treatments which consider various classes of residues as ionizing independently will not give approximately correct relaxation spectra. A model which takes into account the coupling between the degrees of ionization of the various residues is found to give rough agreement with the observed acoustic absorption in the pH range in which the native conformation is stable.
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    Masthead (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.1972.360111001
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    The Role of ions in the acid melting of DNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2033-2041 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of a simple chemical equilibrium and of the law of mass action leads to correct prediction when applied to the study of the role of the counterions in the process of acid melting of the DNA molecule. This approach allows an estimate to be given of the enthalpy variation per base pair associated with this process. Experiments have been carried out to test (a) the linearity of the dependence of pHm vs. 1/T; (b) the stabilizing effect of Na+ concentration. The enthalphy variation per base pair, deduced from the slope of the pHm vs. 1/T plot, and from the number of H+ bound per base pair, is in agreement with direct measurement.6,8
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    Magnitude of a finite equilibration effect in analytical gel chromatography (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2125-2130 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Previous analyses of solute behavior in analytical gel chromatography1,2 have allowed for a finite equilibration time between stationary and mobile phases in estimating the magnitude of axial dispersion coefficients, but have ignored these effects in formulating the continuity equations for solute transport. We develop a more accurate theory including the equilibration effect, and show experimentally that it can be disregarded after approximately two minutes from the start of a small-zone experiment.
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    Hydration mobility in peptide structures (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2179-2186 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structural behavior of hydrochlorides of poly-L-lysine and tetraglycine depends on water vapor pressure. At low relative humidities, structural rearrangements are slow. Water molecules catalyze these structural rearrangements; thus, in tetraglycine 1 H2O molecule per 10 peptide residues. Some general aspects of the mechanism of the hydration mobility in peptide structures are discussed.
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    Naegeli amylodextrin and its relationship to starch granule structure. II. Role of water in crystallization of B-starchJournal Paper No. J-7181 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Proj. 1847. Supported in part by a grant from the Corn Refiners Association and by grant GM 08822 from the National Institutes of Health. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2241-2250 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Although native B-type starch loses its sharp X-ray pattern on strong drying, the wet Nägeli amylodextrin prepared from such starch gives a sharp B-pattern, that is only slightly reduced in sharpness by complete drying. Nägeli amylodextrin dried admixed with a noncrystalline “filler” (e.g., starch sirup) gives an X-ray pattern essentially identical to that of the wet amylodextrin, except that the 16-Å (No. 1) ring is greatly reduced in sharpness and intensity. Failure of the B-structure to collapse during drying indicates that water is not intercalated between turns of a helix or otherwise required to maintain the geometry and packing arrangement of the starch molecular chains. Rather, for native starch granules or amylose fibers, water relieves intercrystallite strains and consequent crystallite distortion induced by strong drying. For Nägeli amylodextrin, the small molecules of starch sirup can penetrate the interstices between crystallites and prevent strain build-up during drying. For native starch granules, the interstitial regions are gel-like in character and less permeable to starch sirup molecules. A model for B-starch is proposed, that employs intertwined (double) helices.
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    Effwct of temperature on the circular dichroism spectra of polypeptides in the extended state (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2309-2316 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism (CD) spectra of poly-L-proline and of poly-L-glutamic acid and poly-L-lysine in their charged states have been studied as a function of temperature. The variation of CD spectra with temperature is inconsistent with the assignment of the spectrum of such charged polypetides to an unordered chain conformation, but does support our earlier assignment to a locally ordered structure - what we have called the extended helix conformation. These results also strengthen our previous assignment of the CD spectrum of an unordered chain, and indicate that three conformational states (α-helix, extended helix, and unordered) should be incorporated in our thinking about conformational transitions in polypeptides.
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    Far from equilibrium synthesis of “prebiotic” polymers (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2349-2356 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The existing experimental data on prebiotic nonenzymic biopolymer synthesis is used to construct a model which shows autocatalysis and highly nonlinear behavior. It is shown that far from thermodynamic equilibrium such systems may exhibit multiple steady states favoring the enhancement of the polymer population in the medium. The role of step by step chain propagation and template directed autocatalysis are studied and contrasted.
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    Volume effects in aqueous solutions of macromolecules containing non-polar groups (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2357-2364 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Specific volumes at 25° of aqueous solutions of poly(N-methyl acrylamide) and poly-(ethylene oxide) have been measured, and the data obtained is compared with corresponding data on low-molecular-weight compounds. The results support the notion, that the volume changes following the interaction between aliphatic groups and water are positive. They are discussed with particular reference to pressure effects on protein conformations.
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    Rapid kinetic studies on the conformation of single-stranded DNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2365-2379 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational states of single-stranded calf thymus DNA were probed using the tmeperature-jump kinetic technique. A rapid decrease in transmission at 260 nm followed by a broad relaxation spectrum was observed for single-stranded DNA at 0.15M KCI, pH, 6.5 at 25°. The relaxation spectrum could also be detected as a hydrogen ion release. Sonicated samples of 103,000 daltons showed identical relaxation kinetics as unsonicated samples. The relaxation kinetics were studied as a function of temperature, pH, and salt concentration and could be interpreted as representing the melting of short, isolated folded segments. The rapid process that could not be kinetically resolved is interpreted as single-strand unstacking. Upon the addition of excess MgCl2 at pH 7.0, a hydrogen ion release from single-stranded DNA was observed that was 3.5 times greater than that observed for a comparable sample of native DNA. Evidence is presented which indicates that charge-pairs exist in folded segments that are A-T rich. There was no kinetic evidence of structures in single-stranded DNA other than single-stranded stacking and short isolated folded regions.
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    Poly(L-alanine): Investigation of alpha-helix and betal-sheet forms by low-temperature specific heat measurements (1.5-20°K) (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2483-2491 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: For an ideal one-dimensional solid, the low-temperature specific heat, C, is proportional to temperature T1, for an ideal two-dimensional solid C is proportional to T2. We have observed such one- and two-dimensional behavior in alpha- and beta-poly(L-alanine) in the temperature range 1.5-20°K (also intermixed with a three-dimensional behavior). A specific heat anomaly has also been observed. These measurements are important in evaluating the effective elastic constants, including hydrogen bonding, of the biopolymers. They also provide essential information for vibrational theories of poly(L-alanine), which up until now have been based on high-energy data.
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    Protein labeling by acetylation (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2533-2536 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method has been developed for labeling proteins by acetylation without appreciable loss in biological activity.
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    Electrical conductivity in the solid state of sodium salts of calf thymus DNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2563-2575 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: A dc conductivity study of native and denatured samples of sodium salts of calf thymus DNA in the solid state was performed at different temperatures and water content. From the results obtained it appears that the major carrier of conductivity is either electronic or ionic, depending upon the temperature of the sample, the water content, and the fact that the conductivity of native samples is higher than that of the denatured ones. These results have been confirmed by dc conductivity studies of poly U and poly A.
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    Hydrodynamic shear breakage of DNAContribution No. 4515 (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2601-2624 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The rate of breakage of duplex DNA molecules by laminar flow through a capillary has been studied. For λb2b5c DNA (molecular wt., M = 25 × 106) the point at which breakage occurs is normally distributed around the center of the molecule with a standard deviation of 12.5% of the molecular length. At constant shear stress or shear rate, the breakage rate is independent of ionic strength. Thus, shear induced local denaturation is not a rate limiting, preliminary step in breakage. In experiments at constant temperature with varying solvent viscosity (controlled by added sucrose) the breakage rate is a function of shear rate, not of shear stress. The rate of opening of hydrogenbonded circles into linear molecules by hydrodynamic shear is also shown to be a function of shear rate and not of shear stress. The breakage rate at constant shear rate is not greatly dependent on temperature. The shear rate required to achieve breakage is inversely proportional to M1,2. The breakage rate constant, k varies as a very high power of the shear rate; at 25°C, d In k/d In Gm ∼ 15; at 10°C, d In k/d In Gm ∼ 26, where Gm is the maximum shear rate at the capillary wall. The unexpected result that breakage rate is mainly dependent on shear rate, not shear stress, supports a model in which the DNA molecule is distorted with a driving force which depends on the hydrodynamic shear stress, ηG, but the rate limiting step is segment diffusion into a highly extended configuration. The characteristic time to achieve this configuration is proportional to solvent viscosity, η, hence the breakage rate is dependent on ηG/η or G, the shear rate.
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    Comparison of the UV flow dichroism spectra of TMV and several of its mutantsThis is Publication No. 190 of the Department of Biophysics and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2393-2413 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dichroic ratio spectra of TMV and four of its mutants (YTAMV, GTAMV, HR, and CV4) were determined from 320 to 240 nm. Measurements were also made on particles of ATMV (TMV protein reconstituted with polyadenylic acid) and rods of repolymerized TMV, YTAMV and GTAMV protein, respectively. These cylindrical molecules were oriented in a flow gradient with their degree of orientation being determined from anisotropic light scattering measurements. Taking length distributions into account, the dichroic ratios were then extrapolated to values characteristic of perfect particle alignment.Due to the large number of overlapping absorbing bands in the whole viruses, it is very difficult to separate out specific contributions to the total spectra. Since, however, the spectra for the whole viruses were similar, this would suggest an overall likeness in structure for all the virus particles studied. Because the repolymerized proteins did not have the four RNA chromophoric groups present, their spectra would be more sensitive to protein contributions to the total spectrum. Repolymerized rods of YTAMVP yielded results similar to those for TMVP, while the spectrum for repolymerized rods of GTAMVP was significantly different from that obtained for TMVP.Dichroic ratio spectra of the nucleic acids, as they exist within the whole particles, were also calculated by subtracting protein absorptivities from their respective viral absorptivities. The spectra indicates similar results for the various nucleic acids in all the particles studied.
    Additional Material: 11 Ill.
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    Effect of organic solvents on the properties of the complexes of DNA with proflavine and similar compounds (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2439-2459 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In order to obtain information on the binding forces involved in the formation of the complex proflavine-DNA by the stronger process I, the stability of the complexes was investigated in the presence of various organic solvents, methanol, ethanol, n-propanol, isopropanol, formamide, dimethyl sulfoxide, p-dioxane, glycerol, and ethylene glycol. Quantitative data on binding in terms of K/n and r were obtained by means of absorption and fluorescence spectra, as well as by a thermal denaturation technique.All organic solvents used decrease the binding ability of the dye. The effectiveness of the solvents increases with their hydrocarbon content, but can hardly be related to their dielectric constant. The complex formation is effectively suppressed by organic solvent concentrations, in which DNA still preserves its double-helical conformation. These results demonstrate the importance of hydrophobic forces in the formation of the complex proflavine-DNA in aqueous solution.The similarity in spectroscopic properties of proflavine bound to DNA by process I and the same dye dissolved in an organic solvent make it possible to interpret the observed red shift of the long-wavelength absorption peak as being due to the interaction of the dye molecules with the less polar environment.The same behavior was found for other dyes capable of intercalation like purified trypaflavine, phenosafranine and ethidium bromide. However, intercalation is not a necessary condition, as it was shown in the case of pinacyanol, which binds only at the surface of DNA.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360111206
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  • 89
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    Thermal transitions in gelatin: Optical rotation and enthalpy changes (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2521-2532 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Enthalpy changes [as determined by differential scanning calorimetry (DSC)] and optical rotation changes over the helix → coil transition were measured for various gelatin solutions and films. From these studies it has been concluded that: (1) a linear correlation between ΔH and Δ[α] exists for gelatin solutions, independent of the temperature at which gelation occurred; (2) the amount of triple helical structure regained when a melted gelatin solution is quenched can be calculated from DSC data, but the values obtained will be dependent on assumptions about the number and strength of hydrogen bonds; (3) the anomalously high levorotation values found for cold-dried films of gelatin do not reflect the presence of an extraordinarily large amount of triple helical structure; rather, the large rotations appear to be the result of orientation of helices in the plane of the film.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360111211
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  • 90
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    Adsorption of single-stranded and double-helical polynucleotides on the mercury electrode (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2577-2589 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The adsorption of single-stranded polynucleotides and double-helical DNA on the dropping mercury electrode has been studied with the aid of Breyer's alternating current (a.c.) polarography. Our results indicate that all three constituents of polynucleotides (residues of bases, sugar, and phosphoric acid) are involved in the adsorption. At neutral pH their participation in adsorption depends on the ionic strength, the potential of the electrode, and the conformation of the polynucleotide in the solution.At an ionic strength of about 0.1, double-helical DNA is adsorbed electrostatically on a positively charged electrode surface by inadequately masked negative charges of the phosphate groups. At a higher ionic srength (about 0.5), this electrostatic adsorption is no longer detectable by using a.c. polarography; under these conditions it is probable that native DNA is adsorbed around the potential of the electrocapillary maximum with the aid of sugar residues and a few bases. Single-stranded polynucleotides, on the other hand, are primarily adsorbed by means of the bases.Desorption of double-helical DNA occurs around a potential of -1.2 V against SCE. At this potential, the helical regions of single-stranded polynucleotides are also desorbed. Desorption of the disordered regions of single-stranded polynucleotides occurs at more negative potentials. Adsorption and desorption of a small number of bases released from double-helical DNA was evident in the a.c. polarograms only at elevated temperature, or at room temperature after degradation of DNA by sonication.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360111215
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  • 91
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    Helical conformations in acidic polysaccharides in solution (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 2625-2631 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360111218
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  • 92
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    Masthead (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110101
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    Spatial configurations of polynucleotide chains. III. PolydeoxyribonucleotidesFrom the thesis submitted by Wilma K. Olson in fulfillment of the requirements for the degree of Doctor of Philosophy, Stanford University, 1971. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 57-66 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean-square end-to-end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C3′-O3′ bond of the deoxyribose residue in the C2′-endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r2〉0/nl2 calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C3′-endo conformation and ≈21 with all residues in the C2′-endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C3′-endo and C2′-endo conformational isomers present in a ratio of ∼1 to 9.
    Additional Material: 5 Tab.
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    Potentiometric titration of polyelectrolytes having stiff backbones (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 137-144 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The potentiometric titration curves of carboxymethylcellulose, which has a relatively stiff backbone, and also of poly(D-glutamic acid) in the helical region are compared with the theoretical curves calculated assuming that the polyions are rods and have smeared charges on their surfaces. For carboxymethylcellulose good agreement is observed when its charge density is high, whereas as the charge density decreases the calculated curves deviate from the observed ones. The main reason for the disagreement at low charge densities may be attributed to the flexibility of the polymer backbone. For helical poly(D-glutamic acid) satisfactory agreement between calculated and observed curves is found if a radius thicker than the realistic radius is employed. The reason for the excessively large radius may be attributed to the inapplicability of the smeared charge model.
    Additional Material: 4 Ill.
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  • 95
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    Semiempirical energy calculations on model compounds of polypeptides. Crystal structures of DL-acetylleucine N-methylamide and DL-acetyl-amino-n-butyric acid N-methylamide (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 105-117 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The sum E of the packing and conformation energies of the crystals of DL-acetylleucine N-methylamide (ALNMA) and DL-acetyl-α-amino-n-butyric acid N-methylamide (ABAMA) is calculated as a function of the crystallographic parameters and the conformational angles. The intermolecular energy is assumed to be the pairwise sum of nonbonded and electrostatic atomic interactions, while both these terms and intrinsic terms describing barriers of internal rotation contribute to the intramolecular energy. For ALNMA E is minimized with respect to 18 parameters: the minimum found when starting from the experimental structure agrees with this within 0.07 Å and 3°, except for one angle which deviates by 6° the average deviations of the atomic coordinates are \documentclass{article}\pagestyle{empty}\begin{document}$ |\overline {\Delta x|} = 0.02,|\overline {\Delta y|} = 0.07,|\overline {\Delta z|} = 0.08 $\end{document} Å. Another minimum with about the same energy shows slightly worse agreement. A comparison between different sets of nonbonded functions is made. The prediction of conformation and intermolecular packing of ABAMA is attempted on the basis of the knowledge of the unit cell and the space group. In agreement with available experimental data it is found that only one-di-mensional arrays of molecules linked by pairs of hydrogen bonds are compatible with the unit cell. The more stable of two possible conformations of the main chain agrees approximately with the experimental conformation. The calculation is not conclusive with regard to the side-chain conformation and the packing of non-hydrogen-bonded molecules.
    Additional Material: 2 Ill.
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  • 96
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    Syntheses and conformational studies of poly-β,N-alkyl L-asparagines (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 185-196 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several β,N-alkyl L-asparagines were prepared from the phthalyl and benzyloxycarbonyl derivatives. High-molecular-weight poly-β,N-benzyl L-asparagine and poly-β,N-(1)-phenethyl L-asparagine were prepared from the corresponding N-carboxyanhy-drides. From the results obtained by a study of the infrared absorption spectra and the optical rotatory dispersion, poly-β-N-benzyl L-asparagine was found to be a random coil structure in dichloroacetic acid and the optical rotatory dispersion curves gradually changed into the left-handed α-helix structure when chloroform was added to the solution. The coil-to-helix transition was observed in the vicinity of 20% dichloroacetic acid in a dichloroacetic acid-chloroform mixture. Poly-β,N-(d), (l), and (d + l, 1:1)(d + l, 1:1): mixed polymer containing the same weighed poly-β,N-(d) and (l)-(1)-phenethyl L-asparagines.-(1)-phenethyl L-asparagines showed a nearly constant specific rotation in the dichloroacetic acidchloroform solvent system. Poly-β,N-(dl)-(1)-phenethyl L-asparagine caused a gradual folding of the helix at dichloroacetic acid content of less than 20%.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110114
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    The nature of stacking equilibria in polynucleotides (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 235-250 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Temperature melting profiles of adenylyladenosine and cytidylylcytidine were examined by ultraviolet absorption, circular dichroism, and optical rotatory dispersion. They showed the following characteristics: profiles for different absorption wavelengths are identical as defined by least-squares computed optical and thermodynamic parameters; melting curves obtained by the three spectroscopic methods are likewise in all cases identical by a series of criteria; in terms of the operational equilibrium constant for base-stacking all van't Hoff plots are linear; absorption spectra and circular dichroism curves at a series of temperatures for both dinucleoside phosphates give excellent isosbestic points; a matrix-rank analysis of the family of complete spectra at different temperatures gives a value of two for the numbers of components in both cases. Four criteria are thus fulfilled of a two-state system for the stacking equilibrium. The results are not compatible with a multi-state scheme in which the substates are optically distinguishable. There is no measurable effect of ionic strength up to 1.0. In a presence of high concentrations of lithium chloride the criteria for two-state behavior are no longer fulfilled, and examination of infrared spectra gives evidence of complex formation by this salt, though not by sodium chloride. A destacking profile, similar to that observed on heating, is obtained by progressive addition of ethylene glycol to the solution. It is suggested that in dimers, though not in higher oligomers or polymers, the stacking equilibrium can be operationally regarded as a two-state system, and that the meaningful thermodynamic parameters can be extracted by analytical treatment, of the type here developed, of the melting profiles.
    Additional Material: 11 Ill.
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    Masthead (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110201
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  • 99
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    Proflavine binding to yeast rRNA and ribosomes as related to structure (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 361-374 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proflavine binding experiments were carried out with yeast rRNA, native and “unfolded” ribosomes; the binding constants and the number of binding sites were calculated by a spectroscopic method. The study of the intercalation complexes by fluorescence and electric dichroism shows the intercalation binding sites to involve two subtypes of sites, which could be related to different nucleotide composition and secondary structure of the rRNA regions, i.e., binding sites located in the (A + U)-rich single strands and binding sites located in the (G + C)-rich double-helical strands (fluorescence quenching sites). Electric dichroism of complexed proflavine is interpreted in terms of rRNA conformation within the ribosomes. The conclusions are in agreement with the ribosomal model of Cox and Bonanou and show that, according to this model, the base planes of the nucleotides are not all parallel in the native ribsome, but rather radiate around the folding axis of the ribonucleoprotein sheet.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110205
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  • 100
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    The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1235-1258 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present CD spectra of four trinucleoside diphosphates, UpUpG, GpUpG, ApUpA, and ApUpG, of four single-stranded polymers, poly AC, poly GU, poly AU, and poly AdU, and of five double-stranded polymers, poly A:U, poly G:C, poly AU:AU, poly AdU:AdU, and poly GC:GC. The measured spectra are compared with empirical firstneighbor calculations. Our results, taken together with data from the literature, suggest that UpA and UpG sequences are relatively unstacked in a single-stranded RNA compared with these isolated dimers in solution. These sequences may influence the structure and function of natural RNAs. Our results on double-stranded RNAs indicate that the spectral changes which occur upon formation of a double helix are unique to the type of base pair involved and are relatively independent of sequence.
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    URL: http://dx.doi.org/10.1002/bip.1972.360110609
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