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  • Polymer and Materials Science  (4,769)
  • Biochemistry and Biotechnology
  • 1980-1984  (3,367)
  • 1965-1969  (1,798)
  • 1960-1964
  • 1925-1929
  • 1981  (3,367)
  • 1968  (1,798)
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  • 1980-1984  (3,367)
  • 1965-1969  (1,798)
  • 1960-1964
  • 1925-1929
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  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In aqueous solutions of the amylase-iodine complex the concentration of free iodine [If]v after reaching equilibrium (or closely approximating it) is determined by the following factors: temperature, pH, concentration of iodide ions and amylose, and DP of amylose. In the present paper the role of temperature, amylose concentration, and DP has been investigated. At half-saturation of amylose by iodine, the reciprocal value of free iodine defines the equilibrium constant: 1/[If]v = K. The relation between [If]v, in normality and temperature is the following: 5 + log [If]v = -(2.132/T) + 8.52, for DPn = 1290, 0.4 mg. amylose in 100 ml. 0.1N HCl. The value of the energy of activation Ea between 2 and 52°C. is 9.72 kcal./mole. The influence of amylose concentration [Am] on photometrically determined [If]v, at 20°C, in the range of 0.1-1.2 mg./100 ml. 0.1 N HCl for DPn = 1290 is: 5 + log [If]v = 0.209 - 0.047 log [Am]. At [Am] = 0.6 mg. amylose/ 100 ml. 0.1 N HCl and 20°C, the value of [If]v depends on DPn as follows: 5 + log [If]v = 0.085 = + 0.222 log (104/DPn). These above equations are summarized by the relation: [If]v = exp {16.865 - (Ea/RT)}[Am]0.047(104/DPn)0.222 ×10-5 Considering that the determination of [If]v by automatic photometric titration can be performed quickly and with appropriate reproducibility, this method is convenient for a rapid empirical and approximate determination of DP of amylose on a microscale. The iodine-binding capacity [IBC] as well as the value of λmax, have been also investigated as functions of DPn, by photometric and by amperometric titration.
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  • 2
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    New York : Wiley-Blackwell
    Biopolymers 6 (1968), S. 415-430 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The transient electric birefringence behavior of bacteriophage T2 and the T2 ghost or protein coal was studied. The field free relaxation measurements show both the intact virus and its ghost to have two rotary diffusion coefficients. These coefficients have values of 555 ± 54 and 111 ± 22 sec.-1 for the intact virus and 688 ± 89 and 161 ± 29 sec.-l for the ghost. The equivalent ellipsoids for the fast and slow relaxation coefficients were obtained by use of Perrin's equation and were related to the bacteriophage structure in terms of a possible extension of the tail fibers or an enlargement of the head structure. The saturation of the specific birefringence of the phage and the ghost when compared with the specific birefringence of the free nucleic acid gave an average optical orientation of 10 to 18% of the nucleic acid parallel to the main axis of the phage. The analysis of the birefringence versus applied field strength in the Kerr region gave the following values for the anisotropy of the polarixability. αe,33 - αe,11 and intrinsic dipole, μ, of both phage and ghost : for T2 phage αe,33 - αe,11 = 5.0 × 10-14 cm.3 and μ = 64,400 Debyes; for T2 ghost αe,33 - αe,11 = 7.9 × 10-14cm.3 and μ = 57,200 Debyes. The high intrinsic dipole for phage and ghost is interpreted as to be associated with the mechanisms of the virus for attachment, to the host cell wall.
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  • 3
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    Biopolymers 6 (1968) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 4
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    Biopolymers 6 (1968), S. 431-440 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hydration of several polyacids has been investigated with special attention to the effects of neighboring charged groups and hydrophobic groups on the hydration regions. The molar volume change due to the structural change of water by the hydration was obtained by the method of refractivity measurement. The polyacids employed were poly(acrylic acid), poly(methacrylic acid), poly(L-glutamic acid), and a copolymer of maleic acid and vinyl acetate. The measurement of the refractive index was performed for the solutions of these polymers neutralized to varying degrees by tetrabutyl-ammonium hydroxide and sodium hydroxide. The results confirm the characteristics of the previous model of the hydration of polyelectrolytes, that is, the cooperative action of neighboring charged groups induce the second hydration region in addition to the intrinsic hydration region. The stiff structure of water in these regions restricts the mobility of counterions forced to enter into these regions by the strong electrostatic potential of polyions. The results indicate also that hydrophobic groups induce an additional hydration region around their neighboring charged groups. Small but negative volume changes were observed for conformational changes of poly(L-glutamic acid) and poly(methacrylic acid) induced by the neutralization of carboxyl groups.
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  • 5
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    Biopolymers 6 (1968), S. 441-448 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The heat of solution of a series of three polyglutamates as a function of solvent composition was measured. The abrupt increase in heat of solution at the solvent composition of the helix-coil transition (as evidenced by optical rotation data) allows the estimation of the transition enthalpy change. The difference of side chain in the three polyglutamates has no appreciable effect on the transition enthalpy, although it affects the helix stability, as judged from the solvent composition at the transition points. These facts are discussed on the basis of existing models of the transition.
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  • 6
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    Biopolymers 6 (1968), S. 469-477 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Single crystals of poly(γ-benzyl L-glutamate) were formed by epitaxial crystallization from solution in mesitylene on NaCl, KI, and KCl (001) cleavage faces. From electron microscopy and diffraction studies, the structure of these overgrowths was determined to be that of lamellae containing chain-folded α-helical macromolecules. The usual type of crystal perfection, that of ordered helix axes and disordered side groups, was exhibited by this synthetic polypeptide. Unique orientation regimes were observed with each substrate.
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  • 7
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    Biopolymers 6 (1968), S. 479-490 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As a model for a variety of reaction processes on long chain molecules, for example, helix formation, a kinetic theory on a linear lattice is presented. Each reaction site can undergo reversible transitions between two states (0 and 1) with rates depending on the slate of its nearest neighbors. The system of coupled rate equations for the frequencies of specified runs of 0's and 1's is infinite for an infinite chain. In contrast to the case of irreversible processes, the system cannot, be written down by inspection. A procedure for the systematic derivation of the rate equations is developed which can be programmed on a computer. Explicit expressions for runs up to length four, involving runs up to length five are obtained without recourse to the computer. For the solution of the rate equations a closure must necessarily be imposed, and a possible procedure is pointed out. Furthermore the equilibrium relations following from the model are considered. The well-known equilibrium results for nearest-neighbor interactions represent a special case of these equations.
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  • 8
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    Biopolymers 6 (1968), S. 1355-1377 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of specific heat of wool-water systems were made at approximately 5°C intervals over the temperature range -70 to 100°C. Ten different, samples were used, each with a different amount of absorbed water in the range from dry ness to saturation at 0°C. The graph of specific heat against temperature for dry wool is precisely linear over the complete temperature range, suggesting that thermal motion is entirely vibrational. When absorbed water is present the data can be conveniently discussed in terms of behavior below and above an amount of absorbed water of 22.7 g in 100 g of wool (22.7% of absorbed water). Below 22.7% there is only one temperature range in which the results indicate an appreciable transition in heat absorbing properties. The temperature of transition depends on water content but is higher than 0°C. Above 22.7% a second transition appears in the range -30 to 0°C and grows rapidly larger with increase of water content. The first transition is tentatively ascribed to a slightly cooperative breakdown of polar bonds in wool, and the second to a process analogous to melting in the absorbed water. The results are discussed in these terms as well as with reference to specific heat theories, the heat absorption of the wool component and the water component, and enthalpy differences between the various samples.
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  • 9
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    Biopolymers 6 (1968), S. 1379-1382 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 10
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    Biopolymers 6 (1968), S. 1383-1386 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 11
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dielectric relaxation of poly(γ-benzyl L-glutamate) in solution has been studied in the 5 kcps-10 Mcps range for various values of the helix content. The results give first experimental evidence for three effects of major significance. (1) The system exhibits dielectric relaxation due to a chemical rate process (namely helix formation). This confirms recent theoretical predictions. (2) The mean relaxation time τ* of the helix-coil transition could be evaluated as a function of the degree of transition. The results are in excellent agreement with a previously developed theory. At the midpoint of transition it is found τ*max = 5 × 10-7 sec. The elementary process of helical growth turns out to be practically diffusion-controlled (with a rate constant of hydrogen bond formation of 1.3 × 1010 sec-1). (3) There is a considerable electric field effect of the helix-coil transition. This indicates that conformation changes in biological systems could be potentially caused by direct action of an electric field.
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  • 12
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    Biopolymers 6 (1968), S. 1387-1388 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 13
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    Biopolymers 6 (1968), S. 983-991 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of unsubstituted purine with polyuridylic acid in D2O solution at neutral pD has been studied by high resolution proton magnetic resonance spectroscopy. The poly U proton resonances were shifted to higher fields by the added purine, indicating that purine binds to the uracil bases of the polymer by base stacking. Severe broadening of the purine proton resonances was also observed, providing strong evidence for the intercalation of purine between adjacent uracil bases of the polymer. The line widths of the poly U proton resonances were not noticeably broadened in the presence of purine; thus, the binding of purine to poly U does not result in a more rigid or ordered structure for the polymer.
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  • 14
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    Biopolymers 6 (1968), S. 997-1000 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 15
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    Biopolymers 6 (1968), S. 1001-1004 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 16
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    Biopolymers 6 (1968) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 17
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polyelectrolyte expansion effects on high molecular weight bacteriophage DNA have been studied by examining the influence of simple salt concentration upon the intrinsic viscosity, [η]. The viscosity-molecular weight exponent a in the expression [η] = KMa diminishes from 0.8 in 0.005M simple salt to a limiting value of 0.6 for salt concentrations greater than 0.6M at 25°C. The ε parameter of the N1+ε hydrodynamic representation thus varies from approximately 0.2-0.07 over this range of salt concentration. The intrinsic, viscosity of DNA decreases slightly with increasing temperature at low and moderate salt concentrations but becomes independent of temperature at high salt concentrations. The expansion of the DNA molecular domain is linear in the reciprocal square root of the simple salt concentration. Viscosity differences among DNA's isolated from several bacteriophage T5 mutants reflect small differences in molecular weight which are in agreement, with sine determination by other techniques. The DNA's isolated from various rII mutants of T4 bacteriophage including some very large deletion mutations were found to be identically the same size in accord with current genetic ideas. Details of the representation and extrapolation of viscosity data are discussed and the sensitivity of the technique is evaluated.
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  • 18
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    Biopolymers 6 (1968), S. 1037-1076 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Infrared spectra in the region 4000-60 cm-1 have been measured for acetylglycine N-methylamide and its deuterium homologs, CD3CONHCH2CONHCH3, CH3-CONHCD2CONHCH3, CH2CONHCH2CONHCD3, and CH3CONDCH2CONDCH3. Normal frequencies have also been calculated for these molecules with various conformations. The spectra show that this compound has two crystalline modifications, form A and form B. The frequencies and their isotope shifts show that the molecular conformation (Ψ, φ) of form B is near (0, 120) and that of form A near (180, 120). The short-range factors determining the conformation of peptide backbone having glycine residues are discussed.
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  • 19
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The objective have been to establish if those ions which are known to change the stability of the structure of proteins, have any influence on the properties of ionizable polypeptides. Potentiometric titrations and complementary optical rotation data are presented for aqueous solutions of poly-L-lysine (PLL) in the presence of KSCN, KCl, and KF, and for poly(L-glutamic acid) (PLGA) in the presence of KSCN, KCl, and LiCl. The following measured quantities which are affected by salt concentration were obtained: intrinsic pK (pK0), slope of pKapp versus degree of ionization (α) curves, the degree of ionization at which the helix to coil transition occurs, and the free energy of this transition for the uncharged molecule (δG°hel). The effects of nonspecific salts (KCl and LiCl for PLL and KSCN and KCl for PLGA) are small, and about, as expected from general electrostatic considerations. In line with the observations made with isoelectric and cat ionic collagen, specific, effects were noted with KSCN-PLL and with LiCl-PLGA. In the presence of KSCN, the poly-L-lysine helix becomes stabilized at much lower degree of ionization than in the presence of KCl, and the slope of the pKapp versus α plots is greatly reduced. However, ΔG°hel (for the uncharged molecule) is not affected, and pK0 is only slightly higher. We interpret these data in terms of binding of SCN- primarily to the side-chain amino groups (both to R—NH3+ and to R—NH2) solutions. (L-glutamic acid) in LiCl solution has its transition at the same α value as in KCl solution. However, both the slopes of the pKapp versus α plots and the absolute values of ΔG°hel are lower than in KCl solution. We interpret these results in terms of binding of Li+ to side chains as well as to the peptide bond.
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  • 20
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Density increments (∂ρ/∂c2)°μ in solutions of NaDNA in NaCl and CsDNA in CsCl were determined over a wide range of salt concentrations; calf thymus DNA, fragmented by sonic irradiation to a molecular weight of 4-6 × 105 was used. The partial specific volume v̄2° of NaDNA at 25°C was found to ho 0.500 ml/g in water, and that of CsDNA 0.440 ml/g. Both values increase with increasing NaCl and CsCl concentration. Refractive index increments under various experimental conditions were also determined. The relevance of the density increments (at constant, chemical potential of diffusible solutes) to equilibrium sedimentation in a density gradient and the evaluation of molecular weights is discussed. Distribution coefficients of diffusible components, sometimes referred to as preferential solvation or net hydration, were derived from the density increments and partial volumes and compared with direct experimental results, whenever available, from membrane distribution and isopiestic distillation. The thermo-dynamic significance of the distribution coefficients as well as possible interpretations in terms of specific molecular mechanisms are considered.
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  • 21
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    Biopolymers 6 (1968), S. 1101-1118 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A model for hemoglobin is proposed and its application to allosteric enzymes is discussed with particular reference to asparate transcarbamylase. The main assumptions made are that the molecule is composed of subunits and that occupation of a sub-unit produces a conformational change which affects the occupational probability of neighboring subunits. The results compare favorably with experiment and a number of specific predictions are made for aspartate transcarbamylase.
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  • 22
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    Biopolymers 6 (1968), S. 1119-1128 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complexes of amylose with n-butanol were prepared both as crystalline precipitates and as oriented fibers. These complexes were subjected to x-ray analysis, their unit cells were calculated, and the space group of P212121 was confirmed. n-Butanol complexes exist in both hydrated and anhydrous forms. There is no evidence for methanol, ethanol, or n-propanol structures similar to those shown by the n-butanol complex. The Complexes are unstable in the open air and revert to V-amylose hydrate on standing.
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  • 23
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    Biopolymers 6 (1968), S. 1147-1158 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Collagen fibers were contracted “chemically,” i.e., by transferring them from water into KCNS solutions either isometrically or isotonically. Both changes in force and fiber length and in salt and water contents were measured as functions of time. The mechanical changes were found to follow the diffusional processes. The diffusion of water exhibited a plasmolytie effect. The role of water in the melting process is discussed.
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  • 24
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    Biopolymers 6 (1968), S. 1129-1145 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The correlation between mechanical and chemical Processes in the contractile system collagen fibers-aqueous KCNS sulutions was investigated. Melting and contraction of the fibers were induced by applying a force sufficiently high as to prevent melting in a KCNS solution and then decreasing it either suddenly, or continuously at a constant rate. The kinetics of both processes are characterized by an initial rapid elastic response of the crystalline collagen, followed by a stationary region. The force-velocity relationship in this region was found to be the same under different types of mechanical deformations. It is probable that under the prevailing conditions, the behavior in the stationary state is determined by the melting process and is not markedly influenced by diffusional changes. Part of the experimental data could be explained by assuming a linear, rigid model or, better, by taking into account the highly elastic properties of the amorphous collagen. The kinetic, unit seems to be composed of several hundred amino acid residues.
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  • 25
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    Biopolymers 6 (1968), S. 1159-1168 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dynamic elastic behavior of collagen fibers treated by LiBr solutions was studied by the method of free longitudinal vibrations. The frequency response functions and the stress-strain relationship were evaluated for fibers denatured to different extents by various concentrations of the salt solution. The James and Guth model for rubber elasticity was applied to the experimental data. The elastometric parameter β, which is a measure of the degree of folding of the macromolecular chains, was found to decrease on increasing the salt concentration. It might thus serve as a characteristic of the degree of denaturation of fibrillar proteins.
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 27
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    Biopolymers 6 (1968), S. 1497-1499 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 28
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    Biopolymers 6 (1968), S. 1500-1502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 6 (1968), S. 1503-1506 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 6 (1968), S. 1507-1508 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 6 (1968), S. 1509-1514 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 6 (1968), S. 1213-1217 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 6 (1968) 
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    Biopolymers 6 (1968), S. 1519-1529 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Sodium hyaluronate (NaHy) and sodium carboxymethyl cellulose (NaCMC) behave similarly with respect to concentration.N 3 of an added 1 : 1 electrolyte. The second virial coefficient A2 (light scattering) is identical within experimental error at a given.N 3. The limiting viscosity number [η] also varies with N3-1/2in similar fashion for samples of similar [η] of the two polymers. Differences in Na+ activity in salt-free solutions are interpreted on the basis of weaker Na+ binding in NaHy, presumably due to the greater charge separation along its chain backbone. Added electrolyte is excluded in dialysis more strongly by NaHy (or its acid form) than by NaCMC. The Flory parameter Φ is smaller in good solvents for NaHy, as for many other polyelectrolytes, than for nonionic polymers.
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  • 35
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    Biopolymers 6 (1968), S. 1551-1571 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In order to test theoretical predictions that poly-L-valine can exist in an α-helical conformation, water-soluble block copolymers of L-valine and D, L-lysine were prepared. By carrying out the synthesis on a resin support (with the use of N-carboxyanhydrides) contamination of the individual blocks by any unreacted monomer from the previous block was avoided. A single glycine residue was incorporated at the C-terminus of the chain for use in amino acid analyses. Using optical rotatory dispersion and circular dichroism criteria, about 50% of the short valine block of (D, L-lysine HCl)18-(L-valine)15-(D, L-lysine-HCl)16-glycine was found to be in the right-handed α-helical conformation in 98% aqueous methanol, in water, the polymer appears to be a dimer, with the valine block being involved in the formation of an intermolecular β-structure.
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  • 36
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations of the dependence of the conformational energy and the rotational strength of the amide n-π* electronic transition (in a series of α-helical polyhel-α- amino acids with different side chains) on conformation have been carried out. The conformational energies were computed by procedures developed in this laboratory; the computation of rotational strengths was carried out by the method of Schellman and Oriel, with a slight modification. Polyamino acids with both nonpolar and polar side chains were considered; in the latter case, it was assumed that the only influence of the polar side chain was on the backbone conformation and on the electrostatic field which perturbs the amide chromophore of the backbone. Only conformations in the range of backbone dihedral angles of the right- and left-handed a-helices were considered, and the assumption of regularity (i.e., uniformity of dihedral angles in every residue) was made. The rotational strength per residue was found to vary markedly with chain length (in oligomers of up to 40 residues long); both the conformational energy per residue and the rotational strength per residue were found to vary significantly with the backbone conformation, which in turn depends on the nature of the side chain. The geometry of the hydrogen bond in the α-helical backbone is the most important factor which influences the dependence of the rotational strength on conformation. The implications of these results, for the interpretation of experimental circular dichroism and optical rotatory dispersion data, are discussed.
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  • 37
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    Biopolymers 6 (1968), S. 1573-1578 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Heat-denatured DNA from HeLa cells interacts with natural as well as synthetic polysaccharides. Glucose does not inhibit the interaction nor will it produce it. Polysaccharides with a molecular weight of 10000 or greater are required before the interaction takes place.
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  • 38
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of copolymers of β-p-nitrobenzyl L-aspartate with β-benzyl L-aspartate and with β-mcthyl L-aspartatc in helix-supporting and helix-breaking conditions have been reexamined by using ultraviolet isotropic, absorption, optical rotatory dispersion, and circular dichroism techniques. Many different conformations are apparent, depending on solvent and temperature. Chloroform, trifluoroethanol, and methylene dichloride support the left-handed helical conformation of the copolymers containing less than about 20 mole-% nitroaromatic residues and the right-handed helical conformation of the copolymers containing more than approximately 30 mole-% nitroaromatic residues. In trifluoroacetic acid all the copolymers are in a random-coil conformation. In hexa-fluoroacetone trihydrate and in trimethyl phosphate, the copolypeptides with low nitroaromatic residues content are predominantly in a disordered conformation, while those with high nitroaromatic residues content show a right-handed helical array. Reversible helix-ramlom-coil transitions are observed with increasing temperature in trimethyl phosphate. An example of right-handed-left-handed helix reversible transition with temperature is reported in a chloroform-trimethyl phosphate (2:1) mixture. Nitrobenzyl-nilrobenzyl side-chain interactions in chloroform, but not in trifluoroacetic acid or in trimethyl phosphate, have been confirmed. For the first time we report the circular dichroism spectra in which the n-π* peptide band of a left-handed helical conformation is almost completely evident.
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  • 39
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    Biopolymers 6 (1968), S. 1605-1631 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dichroic ratios of T5st-O and T2H bacteriophage DNA molecules were measured throughout the ultraviolet region of the spectrum. Two methods of DNA orientation were studied: (1) orientation in solution in a Shimadzu flow dichroism instrument attached to a Beckman DU spectrophotometer, and (2) alcohol precipitation of the DNA from solution and orientation in a thin film on the quartz face of a humidity chamber. Spectra in the latter case were recorded using a Gary Model 14 spectrophotomcter fitted with Glan prisms. The lower wavelength limit was 215 mμ in both systems. The DNA preparations were carefully characterized as to spectral purity, sedimentation coefficient, hyperchromicity, protein content, and DNA content. In addition, the structure of the DNA oriented in films was inferred from x-ray diffraction patterns of fibers of the precipitated DXA. The A and B configurations of DNA in films could not be distinguished by the dichroic ratio measuiements. The dichroic ratio obtained for the film-oriented DNA at high relative humidity shows the same wavelength dependence as for the flow-oriented DNA. The same wavelength dependence for DNA in the fibrous state and in solution, when considered together with the x-ray diffract ion results, indicates that DNA in solution maintains an orientation of bases which is similar to that in fibers. I1Or both solutions and films of DNA, the dichroic ratio is constant from 290mμ to 240 mμ and increases at wavelengths below 240 mμ. The increased parallel absorption below 240 mμ is consistent with the existence of an n→π* transition. The inherent molecular dichroic ratio is found to be the same for T5st-O DNA and T2H DNA in solution, and is a maximum of 0.09 ± 0.02 at 260 mμ.
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  • 40
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    Biopolymers 6 (1968), S. 1633-1647 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper gives a very simple method based on the characteristic property of the electric free energy to calculate the repulsive force between parallel rodlike macroions in a solution as a function of the charge density on rods. The total extensive force (∂f/∂X) of an assembly of m rods of length l and charge number n (charge density - neo /l) at small extension X in the absence of low molecular sals is given by where z is the valency of counterions and Q (= neO2/εkTl) is a dimensionless quantity representing the charge density. The repulsion between two parallel rods is given by putting m = 2. At large charge densities the repulsion is very much smaller than the direct coulomb force between charged rods, even at small distances. The addition of low molecular salts does not depress the repulsion appreciably, as long as the average concentration of salt ions is much smaller than the concentration of counterions accumulated in the space between rods. The effect of fluctuation of the coumerion distribution is also analyzed, and it is found that the attractive force due to the ion fluctuation may predominate over the above repulsive force in the case of polyvalent counterions and rods of high charge densities at small distances.
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  • 41
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    Biopolymers 6 (1968), S. 575-584 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The matrix method of statistical mechanics is used to calculate equilibria for the binding of small molecules to polymers. When there is only one kind of binding site the problem is simple; some examples are given for illustrative purposes. If, however, the binding sites are not all equivalent and the bound molecules interact or interfere with each other, the problem is no longer trivial, being formally analogous with calculation of the helix-coil transition equilibrium in a heterogeneous polypeptide. Particular difficulties arise when the sequence of binding sites is aperiodic; most naturally occurring materials fall in this class. The purpose of this paper is to point out that problems of this type are readily solved with good accuracy by use of random-number methods on a high-speed digital computer. One such calculation is presented for illustration. The methods developed are applicable to such systems as the binding of actinomycin, Hg-, and acridine dyes to DNA.
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  • 42
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aggregated form of poly(L-glutamic acid) can be isolated by gel permeation chromatography, whereby it was found that in a polydispersed sample the lower molecular weight fractions precipitate preferentially and the higher fractions tend instead to aggregate. In addition, aggregation has the effect of retarding or inhibiting precipitation.
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  • 43
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The instability of aqueous solutions of poly(α-L-glutamic acid) (PGA) at low pH is due to two distinguishable phenomena: precipitation, favored above 40°C., and aggregation, favored below 20°C. The aggregated form of PGA can be isolated by gel permeation chromatography. Both aggregation and precipitation increase with decreasing pH, i.e., with decreasing ionization of the side chain carboxyl groups. Temperature-induced aggregation and disaggregation give rise to a reproducible hysteresis loop which can be followed by optical rotation, light scattering, sedimentation, viscosity, and chromatography. Hysteresis has been observed with different PGA samples, and in several aqueous buffered or unbuffered solvents and organic-aqueous solvent mixtures and in the pH range 4.1-4.5. Aggregation manifests itself as an increase in negative optical rotation in the visible and ultraviolet spectral range. The specific relation at 233 mμ is sensitive to aggregation and also reflects the hysteresis. Measurements of optical rotatory dispersion indicate that a0 reflects the hysteresis but b0 does not, the latter revealing only reversible changes with aggregation and disaggregation. The helix-coil equilibrium is apparently unperturbed by aggregation, as is the thermal stability of the helix structure. For fully aggregated PGA it is estimated that a0 increases by about 300 degrees, which suggests that a0 may be a sensitive parameter to measure aggregation in other systems. The rate of aggregation increases with decreasing temperature. The disaggregation, upon heating, is more rapid. However, kinetics measurements have not yet been done. The temperature M at which all aggregates are disrupted increases with decreasing pH, but is independent of total PGA concentration, at constant pH. No molecular weight dependence of M was detected in the range 20-100 × 103. The shape and size of the hysteresis loop depends upon pH and molecular weight, which is interpreted as a dependence on the extent of aggregation. One branch of the loop, representing the helix-coil transition of isolated molecules, is reversible, while the others, representing the formation and disruption of the aggregates, are not. The system exhibits both ascending and descending scanning curves, which are typical of a true hysteresis.
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  • 44
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of hapten (ε-DNP lys) with native and S-sulfonated antibodies specific towards the 2,4-dinitrophenyl group, as well as the interaction with isolated chains and a complex obtained by mixing light, (L) and heavy (H) chains of these antibodies, were followed both by polarography and by equilibrium dialysis. With the S-sulfonated antibodies and with the mixture of H and L chains the binding heterogeneity observed in the original antibodies was much lowered or entirely removed. At the same time, the amount of active proteins in the sample decreased approximately by half. The association constants of modified antibodies were of the same order as the average association constants of the original antibodies. A slow increase of the amounts of hapten bound with proteins was observed on mixing the H and L chains and adding hapten. This slow reactivation was not obtained with the original or S-sulfonated antibodies and with isolated chains. It was shown that the reaction determining the kinetics of this reactivation (the slowest reaction) was not the association of H and L chains but the interaction of complexes of the H and L chains with hapten. It was reported previously that H chains were nonspecifically reactivated by binding L chains. The amount of hapten bound by the complex of H and L chains increased with increasing excess of L chains following a curve resembling the Langmuir isotherm. The limiting value of the amount of hapten bound when using antibody L chains was higher than in the case of nonspecific L chains.
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  • 45
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The rate of breakage by hydrodynamic shear of the cohered ends of λ-DNA molecules has been observed for the circular monomers, joined half molecules, and joined quarter molecules, in a capillary apparatus with known flow parameters. The rate constant for breakage has been measured as a function of shear stress, temperature, ionic strength, and molecular length. There is a large temperature coefficient, with an activation energy of 120 ± 20 kcal./mole. The values of d ln k/dG, where k is the rate constant for breaking and G is shear gradient, in aqueous solution at 25°C. are about 3.8 ± 0.3 × 10-4 see. The shear stresses needed for breakage of joined quarter molecules and of circular monomers, respectively, are about equal, and about half that needed for breakage of joined half molecules. The rate of breakage at a given shear stress increases with decreasing ionic strength, approximately as [Na+]-1.6. Self-protection effects are not observed for opening of circular monomers at a DNA concentration of 5 μg./ml. but are observed for breakage of joined half molecules at concentrations down to 0.5 μg./ml. The large temperature coefficient which is approximately equal to that of the thermal dissociation of the cohered ends is interpreted to mean that shear breakage is a mechanically assisted thermal reaction in which the thermal fluctuations provide most of the free energy of activation for breakage. A detailed model for this interpretation is presented. The self-protection effect implies that those molecules which break are not average molecules but exceptional ones which, due to some fluctuation, are more fully extended in the flow field.
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  • 46
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    Biopolymers 6 (1968) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 47
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    Biopolymers 6 (1968), S. 775-775 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 48
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    Biopolymers 6 (1968), S. 777-791 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dynamic viscoelastic properties of hyaluronic acid solutions have been measured over the frequency range 0.02-1.67 cps. The effects of varying temperature, hyaluronic acid concentration, pH, and ionic strength on the dynamic shear moduli were studied. The solutions exhibited a sharp transition from viscous to elastic behavior as the strain frequency increased. No entanglement coupling of the hyaluronic acid molecules was evident over the concentration range 2.0-4.0 mg./ml. Solutions at pH 2.5 showed a pronounced elastic behavior relative to both higher and lower pH's. This effect was attributed to a stiffening of the hyaluronic acid molecule at this pH.
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  • 49
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    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
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  • 50
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 51
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    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
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  • 52
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
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  • 53
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    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
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  • 54
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    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
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  • 55
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
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  • 56
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    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
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  • 57
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    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
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    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
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  • 59
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 60
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    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
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  • 61
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    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
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  • 62
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
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  • 63
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    Biopolymers 20 (1981), S. 231-235 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 64
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    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 65
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    Biopolymers 20 (1981), S. 243-247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 66
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
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  • 67
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    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
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  • 68
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
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  • 69
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
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  • 70
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    Biopolymers 20 (1981), S. 2121-2136 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
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  • 71
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    Biopolymers 20 (1981), S. 2137-2142 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
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  • 72
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    Biopolymers 20 (1981), S. 2195-2202 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
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  • 73
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    Biopolymers 20 (1981), S. 2225-2241 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present an alternative to the common lattice model for nonspecific DNA-protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one-dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding-site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee-von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single-stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
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  • 74
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
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  • 75
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
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  • 76
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    Biopolymers 20 (1981), S. 2623-2633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-Nmr was used to measure the rate of cis-trans interconversion of X-Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10-3 s-1 at 25°C was found for the zwitterionic form of H-Ala-Pro-OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10-fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C-terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO-Gly-Gly-Pro-Ala-OCH3 to the closely related cyclic compound c[-Gly-Gly-Pro-Gly-Ala-]. These data are evaluated with regard to their possible use in future studies on the role of X-Pro cis-trans isomerization in the kinetics of protein folding.
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  • 77
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As a model compound for the growing chain in the activated-NCA type of polymerization of α-amino acid N-carboxyanhydride (NCA), 3-[ω-acetylglycyl-poly(α-amino acid) acyl]-α-amino acid NCA (called the prepolymer) having various degrees of polymerization (DPs) was synthesized by the polymerization of Phe, Val, Glu(OEt), and Asp(OBzl) NCA in the presence of AcGly NCA by the tertiary amine. Activated (S)-Phe, Val, Glu(OEt), and Asp(OBzl) NCA were added to the terminal cyclic group of the corresponding (S)- or (R)- prepolymer, and the enantiomer selectivity in the reaction was investigated. With prepolymers having DPs ranging from 1 to 15, the addition reaction always took place preferentially between species having the same configuration, and the degree of the enantiomer selection increased with increasing DP of the prepolymer. With prepolymers having DP = 1 and 2, we found contributions from the chiral terminal unit and the chiral penultimate unit to the enantiomer selection, respectively. Prepolymer having DP = 5 was shown to take a β-type conformation, which led to higher enantiomer selection; and prepolymers having DP = 10 and 15 were shown to take an α-helix conformation, which led to much higher enantiomer selection than did the β-type conformation. In the present investigation the mechanisms of terminal-unit control, penultimate-unit control and conformational control of the enantiomer selection in the activated-NCA type of polymerization were clearly observed.
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  • 78
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The helix-coil transition and conformational structure of poly(8-bromoadenylic acid) [poly(8BrA)] have been investigated using 1H- and 13C-nmr, CD, and ir spectroscopy. The results have been compared with the structure of the related 5′-mono- and polynucleotides. The chemical shifts of H(2′), H(3′), C(2′), and C(3′) nmr signals show an interesting correlation with both the puckering of ribose ring and glycosidic bond torsion angle. Poly(8BrA) shows an upfield shift of the C(3′) signal and a downfield shift of the H(3′) signal compared to the chemical shifts in poly(A). These shifts are consistent with a C(3′) endo-syn conformation for poly(8BrA). A similar effect has been reported previously and is also observed here on the C(2′) and H(2′) signals when the preferred conformation is C(2′)endo-syn (e.g., in 5′-8BrAMP). The chemical-shift parameters thus act as a probe for studying syn ⇄ anti and N ⇄ S equilibria in solutions. The three-bond 1H-′13C coupling constants between H(1′) and C(8) and C(4) have been measured in poly(8BrA) and 5′-8BrAMP and their structural implications have been discussed. The observed preference of a C(3′)endo-syn conformation for poly(8BrA), coupled with other evidence, throws doubt on the validity of a correlation previously reported whereby a syn conformation is associated with a C(2′)endo ribose pucker. The backbone conformation of randomly coiled poly(8BrA) is very similar to the structures found in polyribonucleotides: poly(A) and poly(U). All three polymers show strong preferences for the backbone angles found in RNA helices. The CD spectrum of poly(8BrA) has a striking relationship to that of poly(A). The signs of all extrema are inverted, and the magnitudes are related by a constant factor. We suggest that these differences result from a change in the angle between coupled transition moment vectors in the two polymers. Infrared spectra of poly(8BrA) in H2O and D2O solution are reported for the frequency range below 1400 cm-1. The antisymmetric 〉PO2- stretching vibration is observed at an unusually low frequency in the helix (1214 cm-1). The symmetric 〉PO2- stretch occurs at ∼1095 cm-1 but is not resolved from a ring vibration near this frequency. A conformationally sensitive band, characteristic of helical RNA structures, is observed at 817 cm-1 and disappears when the helix is melted. This observation confirms the conclusion that ordered poly(8BrA) has a regular helical structure with an RNA backbone conformation. A stereochemical explanation is provided for the failure of poly(8BrA) (or other syn polymers) to form double helices with anti-polyribonucleotides.
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  • 79
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    Biopolymers 20 (1981), S. 1103-1112 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The arginine and lysine residues of calf thymus histone H1 were modified with large molar excesses of 2,3-butanedione and O-methylisourea, respectively. Kinetic study of the modification reaction of the arginine residue revealed that the reaction is divided into the two pseudo-first-order processes. About a third (1 Arg) of the total arginine residues of the H1 molecule was rapidly modified without causing any detectable structural change of the molecule, and the slow modification of the remaining arginine residues (2 Arg) led to a loss of the folded structure of H1. In the case of lysine residue modification, 93% (56 Lys) of the total lysine residues of the H1 was modified with the same rate constant, while 7% (4 Lys) of lysine residue remained unmodified. When the reaction was performed in the presence of 6M guanidine-HCl, all of lysine residues were modified. It is concluded that the 2 arginine and 4 lysine residues resistant to modification are buried in interior regions of the H1 molecule and play an important role in the formation of the H1 globular structure, while the other 1 arginine and 56 lysine residues are exposed to solvent.
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  • 80
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    Biopolymers 20 (1981), S. 1191-1209 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molar Kerr constants mK, molar refractions mR, and dipole moments μ are reported for the N-methylacetamides CX3CONHCH3 (X = H, CH3, F. CI, Br) and acetamides CX3CONH2 (X = H, F, Cl, Br). The components of the polarizability tensor α are deduced for N-methylacetamide and acetamide on the basis of the bond additivity approximation. This α is found to be considerably more anisotropic than was indicated in previous determinations by other methods. The data for N-methylacetamide were used to calculate mK, μ, and γ2 (anisotropy squared) of N-acetyl-N′-methylglycine amide and N-acetyl-N′-methyl-alanine amide as functions of the torsional angles (φ,Ψ). The statistical mechanical averages of mK, μ, and γ2 were calculated from conformational energies obtained by the methods of Scheraga.
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    Biopolymers 20 (1981), S. 1247-1260 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The physical properties of single, 5-8-μm diameter, water-swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus (G) has a value of 4.1 × 105 N m-2, the average molecular weight of chains between crosslinks is in the range of 6000-7100, and the stress optical coefficient (C′) is 1 × 10-9 m2 N-1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non-Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7-8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
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    Biopolymers 20 (1981), S. 1333-1335 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 83
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    Biopolymers 20 (1981), S. 1399-1411 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Heavy meromyosin binding to F-actin saturated with tropomyosin is studied theoretically. The problem is formulated as a special case of n-mer adsorption to a one-dimensional Ising lattice which is divided into m-site-long blocks.
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  • 84
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    Biopolymers 20 (1981), S. 1481-1502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio 〉 20; 0.1 〈 L/P 〈 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
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  • 85
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    Biopolymers 20 (1981), S. 1537-1547 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at 45°C and then leads to a loss of second-order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10-12% in 2.4M Et4NCl fails to increase the acceleration beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35-40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
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  • 86
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    Biopolymers 20 (1981), S. 1503-1535 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the preceding article, a Monte Carlo analysis was presented which provides a quantitative numerical relationship between the rotational diffusion coefficients, as measured by the decay of optical anisotropy following an electric field pulse, and the flexibility (persistence length) of short, wormlike chains. In the present article, the results of the foregoing analysis are applied to the observed rates of decay of birefringence for a series of sequenced DNA fragments ranging in size from 104 to 910 base pairs. Under the conditions used in this study, the DNA fragments exist as native, duplex molecules. Furthermore, conditions are defined in which the observed relaxation times are not dependent on DNA concentration, field strength, or the duration of the pulse. It is pointed out that the ionic atmosphere associated with a wormlike polyion does not exert any significant (direct) influence on the rotational diffusion of the polyion and, therefore, that the rotational relaxation times are a true measure of the configurations of the DNA molecules in solution. Moreover, excluded-volume effects are shown not to be significant for the moderately short molecules employed in this study. The major conclusion of this study is that there is no strong ionic strength dependence of the persistence length for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å. For ionic strengths significantly lower than 1 mM, electrostatic contributions to the stiffness of DNA become significant.
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  • 87
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    Biopolymers 20 (1981), S. 1575-1588 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aqueous and hydroalcoholic solutions of the heptenic macrolide amphotericin B display strong and variable signals in CD and absorption spectroscopies in the range of the π* ← π transition. An interpretation of the spectroscopic changes is proposed based on the equilibrium between two forms of the intermolecular organization: the aggregated one (A) with strong excitonic interaction and the nonaggregative one (B) whose spectra are like those of linear conjugated polyenes in true solution with a well-developed vibrational structure. The intermediate spectra are fitted by linear combination of the A- and B-form spectra. A two-level organization of the aggregates is proposed for the A-form: (1) a close packing of few molecules, which is the origin of the absorption maxima hypsochromic shift; and (2) interaction between the preceding small units inside the aggregates, which is spectroscopically expressed by the intense CD couplet.
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  • 88
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    Biopolymers 20 (1981), S. 1625-1633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polypeptides of dicarboxylic amino acids having the monomer units linked in α- and ω-peptide bonds contain two kinds of carboxyls of different acidity. How well potentiometric titration can distinguish these two carboxyls and so characterize the nature of the peptide bonds is evaluated critically. An analysis of the equation describing the dependence of pH on the degree of neutralization based on neglecting the polymer effect and a discussion of the dissociation behavior of polyanions show that the method of evaluating experimental data found in the literature is incorrect. Nevertheless, if a conformational transition does not interfere, some useful and reliable information may be gained by this method; namely, an indication of the presence of two different peptide bonds, their mole ratio, and an approximate pK value for the carboxyl of the amino acid linked in the ω-peptide bond. The presence of two types of carboxyls complicates the evaluation of the titration curves in the conformation studies.
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  • 89
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    Biopolymers 20 (1981), S. 1707-1725 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational analysis of antiparallel double-helical polynucleotides with Watson-Crick base pairing was reduced to a four-dimensional problem using original mathematical methods. In the four-dimensional conformational space the family of structures, characterized by the base-pair stacking with the most stable conformations in water solution as well as in the solid state, was localized. For the C′2-endo sugar pucker, both right-handed and left-handed structures were found; right-handed structures only, however, seem to be allowed for the C′3-endo pucker, the only possible one for ribonucleotides with base stacking.
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  • 90
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Angiotensin II and its competitive inhibitor [Sar1, Ile8]-angiotensin II, as well as several analogs of these two compounds specifically chosen for their well-defined pharmacological properties, were studied by circular dichroism and nuclear magnetic resonance methods at various pH values in aqueous solution and in d6-dimethylsulfoxide. The results were compared with their biological activities. This allowed us to establish relationships between conformation and pressor activity, explaining most of the properties of angiotensin II, its inhibitor, and the analogs successively substituted in positions 3 and 5.
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    Biopolymers 20 (1981), S. 2011-2020 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Peptide agonists covalently attached to tobacco mosaic virus exhibit such unusual properties as superpotency, superaffinity, enhanced resistance towards enzymic degradation, and prolonged action at the target cell. These properties can be exploited for the isolation by density-gradient centrifugation of membrane vesicles bearing specific receptors for the peptides and for radioactive and fluorescent labeling of cell-surface receptors. Our observations can be explained by cooperative-affinity phenomena caused by the deployment in space of the agonist molecules.
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  • 92
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    Biopolymers 20 (1981), S. 2035-2049 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The early steps of fibrin aggregation induced by low Reptilase concentrations were studied by means of static and dynamic light scattering. In order to obtain information on the size and shape of the first oligomers, the angular dependence of the scattered intensity and the mean Rayleigh line width were measured. Under physiological pH and ionic strength, oligomer formation was detectable immediately after enzymatic activation. Comparison of the calculated data for different models with experimental results shows that the early fibrin polymerization proceeds as an end-to-end aggregation of elongated and possibly flexible molecules approximately 75 nm long.
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    Biopolymers 20 (1981), S. 2083-2091 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The equivalent conductivity of salt-free solutions of deoxyribonucleates of alkali metals and ammonium obtained by filtering an isoionic DNA solution through a cation exchanger in the corresponding form has been investigated in the concentrations range of 1 × 10-4 to 4 × 10-3M. For all counterions investigated there is a linear dependence of the equivalent conductivity on \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {C_p} $\end{document}, where Cp is the nucleic phosphorus concentration. The limiting equivalent conductivity of deoxyribonucleates increases linearly with the limiting mobility of a counterion. By extrapolation to the zero mobility of the counterion, we have obtained the limiting mobility of a macroion, which is equal to 19 × 10-4 Sm m2 equiv.-1, which is in good agreement with the literature data for denatured DNA obtained by the method of a moving boundary. It is shown that the degree of binding of counterions calculated from the conductometric data in diluted DTA solutions in independent of the nature of the univalent counterion. The degree of dissociation of H+-DNA in the isoionic solution calculated with allowance for the fraction of unprotonated bases practically coincides with this value for salts of DNA. The parameter of Manning's theory calculated from the experimental data corresponds to the distance between phosphates along the chain of the macroion, which is equal to 6.7 Å. We attribute the smaller value of this distance as compared with the theoretical one for denatured DNA to the aggregation of macroions.
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  • 94
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    Biopolymers 20 (1981), S. 2165-2179 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A hydrate of cellulose II can be formed by swelling Fortisan fibers in hydrazine and then washing in water. The hydrate is stable at 93% relative humidity and has a monoclinic unit cell with dimensions a = 9.02 Å, b = 9.63 Å, c = 10.34 Å, and γ = 116.0°; the space group is P21. The unit cell contains disaccharide sections of two chains and approximately four water molecules. The structure was refined using the LALS method, based on 10 observed and 10 unobserved reflections. An antiparallel arrangement of adjacent chains was assumed, since this occurs in cellulose II (the starting material), and the hydrate also reverts to cellulose II on dehydration. Refinement of the positions and side-chain conformations of the chains shows that the chains are stacked in the same way as in cellulose II, and the hydrate is formed by insertion of water molecules between the stacks. However, all efforts to arrange the water molecules in crystallographically regular positions led to unsatisfactory agreement between the observed and calculated intensities. These results suggest an irregular arrangement of the water molecules, which was modeled using water-weighted atomic scattering factors. The analysis resulted in two refined models with relative chain staggers of ∼ +c/4 and ∼ -c/4, which are indistinguishable in terms of the x-ray agreement. Our preference is for the +c/4 model, for which the stacks of chains are analogous to those in cellulose II.
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  • 95
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of calcium ions with α-elastin has been investigated by equilibrium dialysis, CD, and microcalorimetric techniques. Consistent with literature data, it was found that the interaction in water is very poor. In trifluoroethanol (TFE), equilibrium dialysis experiments showed that calcium ions bind to ∼-elastin with an association constant of ∼250 L × mol-1. Such a figure is not consistent with highly specific, highly selective binding. It was also found that the CD response is not directly proportional to the amount of bound calcium but depends on the protein concentration. From microcalorimetric experiments it was found that the heat effect relative to the binding process is of the order of 1.9 kcal/g ion. From this figure and from the binding constant, a positive ΔS value of about 17 e.u. was evaluated, leading to the conclusion that the binding process is entropy driven. From microcalorimetric measurements a ΔH of 1.5 kcal/residue was found for the calcium-induced conformational transition of the protein.
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  • 96
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    Biopolymers 6 (1968), S. 189-213 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Some general rules governing hydrogen bonding at the ring oxygens of furanosides, pyranosides, and bridge oxygens of glycosides have been formulated from existing data on crystal structures of carbohydrates. Ring oxygens of the majority of the glycopyranosides in the hemiacetal or acetal form are involved in hydrogen bonding such that the hydrogen bond direction is usually equatorial to the ring plane and not axial. In contrast, there are no known examples of ring oxygens of glycofuranosides and methyl-glycopyranosides displaying hydrogen bonding in the crystal. Also, the bridge oxygens of glycosides are not involved in hydrogen bonding. The observed shortening in the exocyclic and endocyclic anomeric C(1)—O bonds and the geminal C—O bonds indicate that compounds with two oxygen atoms attached to the same saturated carbon atom may participate in double-bond-no-bond resonance interaction in the same manner as difluoromethane. It is also possible that under these circumstances the carbon atom exhibits greater than tetracovalency. The “anomeric effect” may also be related to (a) the differences in the “double bonding” or bond shortening in the anomeric C—O bonds of the anomeric glycopyranosides, (b) the shorter intramolecular O(1)…O(5) non-bonded interaction, and (c) the smaller O(1)C(1)O(5) valence angle in the equatorial anomer compared to the axial anomer. An analysis has been made of the energetically preferred conformations about the glycosyl and glycosidic bonds of 1,4- and 1,3-polysuc-charides. In the 1a, 4e-glycopyranosides the projected angle φ1 [O(5)C(1)OR, where R = C or H] is positive, while it is negative in the 1e, 4e-glycopyranosides. Angle φ2 [C(1)OC(4′)C(3′)] is positive in both the 1,4-anomeric polyglycosides. 1e, 4e- and 1a, 4e -polysaccharides are stabilized by intramolecular O(5)…H—O(3′) and O(2′)…O(3′) hydrogen bonding, respectively, and generate linear and helical (cyclic) structures, respectively. 1e, 3e- and 1a, 3e-polysaccharides may be stablized by one of two possible intramolecular hydrogen-bonding schemes such that the 1a, 3e -polysaccharides generate helical structures while the 1a, 3e-polysaccharides generate nonhelical structures. The conformation about the C(5)—C(6) bond in the pyranosides falls into two groups where the angle φ00 [O(5)C(5)C(6)O(6)] is either positive, ∼+60 ± 30°, or negative, ∼-60 ± 30°, the former conformation being found more frequently. In the furanosides the latter conformation is preferred.
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    Biopolymers 6 (1968) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 98
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of spermine derivatives (II), \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm R}_1 {\rm R}_{\rm 2} {\rm R}_{\rm 3} \mathop {\rm N}\limits^ + \left( {{\rm CH}_2 } \right)_3 \mathop {\rm N}\limits^ + {\rm R}_{\rm 1} {\rm R}_{\rm 2} \left( {{\rm CH}_2 } \right)_2 ]_2 \cdot 4{\rm X}^ - $\end{document}, and spermidine derivatives (III), \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm R}_1 {\rm R}_{\rm 2} {\rm R}_{\rm 3} \mathop {\rm N}\limits^ + \left( {{\rm CH}_2 } \right)_4 \mathop {\rm N}\limits^ + {\rm R}_{\rm 1} {\rm R}_{\rm 2} \left( {{\rm CH}_2 } \right)_3 \mathop {\rm N}\limits^ + {\rm R}_{\rm 1} {\rm R}_{\rm 2} {\rm R}_3 \cdot 3{\rm X}^ - $\end{document}, are reported. The effects of these salts on the helix-coil transition of rA-rU and rI-rC helices were examined. Increasing the size of the hydrophobic substituents, R1, R2, and R3 lowers the degree of stabilization of the helical structure. The disproportionation reaction, 2rA-rU→rA-rU2 + rA occurs readily with salts II and III, especially when the substituents, R1, R2, and R3 are small, i.e., H or Me. Spermine is found to stabilize the rA-rU2 and rI-rC helices to approximately the same extent; however, large differences between the degree of stabilization of rA-rU2 and rI-rC helices are observed when the substituents R1, R2, and R3 are large hydrophobic groups. Similar results are also obtained for the spermidine series. Finally, differences in the interactions of the salts II and III with rA-rU2 and rI-rC helices suggest that the latter helix is denser.
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    Biopolymers 6 (1968), S. 293-297 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Studies have been made of the d.c. semiconductive behavior of fibers and solid gels of DNA. The semiconductive behavior under high vacuum is similar in solid gels of DNA and stretched fibers of DNA measured along and across the fiber axis. Photoelectric effects have been studied, and an action spectrum is reported which agrees with the absorption spectrum of DNA. No photoelectric effects are observed at wavelengths corresponding to the thermal energy gap. The temperature dependence of the photocurrent has been determined, and the effects of air, oxygen, and nitrogen at different pressures on the photocurrent have been measured.
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    Biopolymers 6 (1968), S. 299-306 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The predominant role of van der Waal interactions in determining the helical conformations of a simple synthetic linear polymer, as well as helical polypeptides, was pointed out in systematic studies by Liquori et al.1,2. In the case of homopolypeptides the conformational analysis carried out on the basis of a simple semiempirical function describing the van der Waal pairwise interactions between the non directly bonded atoms lead to the conclusion that only five helices are allowed (Rα, β, γ, δ, Lα).2,3In view of the close similarities with poly-L-alanine, we have investigated by x-ray and conformational analysis the molecular conformation of poly(S-lactic acid) which has recently been described by Kleine and Kleine4 and Schuls and Schwaab5 and studied in solution by Goodman and D'Alagni.6 In fact, this polymer may be related to the polypeptide by the interchange of a peptide bond with ester bond along the main chain. This operation is expected to involve only a relatively small change in the steric interaction within the possible helical conformation, but obviously rules out any possibility of hydrogen bonding.
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