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  • Wiley-Blackwell  (18,794)
  • 2010-2014
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  • 2010-2014
  • 1980-1984  (16,754)
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  • 1
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 823-831 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of the DNA-binding oligopeptide distamycin A on the B to A transition of DNA in ethanol/water solutions has been studied by means of CD. (The overbars indicate that it does not matter which particular form of the corresponding families is considered.) The results show that increasing the concentration of distamycin A reverses the A conformation (in 82% ethanol) to the B conformation due to its strong binding and stabilization of the latter. In accordance with previous data for pure aqueous solutions, a site size of 3.5 base pairs is obtained from the studies in water/ethanolic solutions. From the data on the B to A transition in the presence of distamycin A, we estimated the length of the cooperativity ν0 = 10 base pairs.The results demonstrate that the oligopeptide systems of distamycin, as well as those of netropsin, are effective stabilizers of the DNA B-conformation.
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  • 2
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N-terminal side, were studied in their various ionic states in 2H2O and in Me2SO-d6 by 1H- and 13C-nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H-1H, 13C-13C, and 13C-1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β-turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3JC3αH-N3H and the 3JC2′-H3α coupling constants, which both furnish a dihedral angle of φ3 = -90°, and from the positive value of the temperature coefficient of the glycine-4 amide protons, which suggests a type 4 → 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side-chain rotamer fractions of the residue in position 3. In the β-turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β-turn.
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  • 3
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An algorithm is presented for the Monte Carlo simulation of the decay of fluorescence polarization from segmentally flexible molecules. Based on the random walk model of Brownian motion, the treatment explicitly follows the stochastic changes in the diffusion coefficients as the molecule bends. It includes the effects of a linear restoring force opposing the bending and the effects of hydrodynamic coupling between the translational, rotational, and bending motions. One application is presented: the simulation of anisotropy decay curves for hinged rods. A variety of decay curves are obtained, including single- and multiexponential behavior, and the following conclusions are reached: (1) increasing the flexibility is usually, but not always, accompanied by a more rapid rate of depolarization; (2) reducing the size of the fluorescent subunit will usually, but not always, increase the rate of depolarization; and (3) the complex interplay between the effects of molecular shape, relative sizes of the subunits, restoring force, and orientation of the transition dipoles renders it unlikely that any simple method can be used to interpret anisotrophy data without simulation. In particular, it is not possible to determine the extent of bending by fitting the data with the two-exponential approximation used by some investigators in the past.
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  • 4
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    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 977-990 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C-nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C-nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6-anhydrogalactose), and the positions of the sulfate and O-methyl groups in a polysaccharide molecule.
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  • 5
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric response of human umbilical cord hyaluronic acid in various environments has been studied at microwave frquencies using a resonant microwave cavity as a probe. Both the real and imaginary parts of complex dielectric constant and the loss tangent for hyaluronate solutions are obtained by utilizing equations for perturbation of a resonant cavity. Dielectric changes at room temperature have been observed in aqueous solutions of hyaluronic acid as a function of concentration ranging from 0 to 350 mg/ml. The data indicate the existence of ordered phases in hyaluronate solutions at selective concentrations, that is, exhibiting lyotropic-type transitions. Hyaluronate solutions at 1.5 and 3 mg/ml concentrations have been studied at various pH in the range of 6-8 and at constant ionic strength 0.1. A temperature-dependent transition in hyaluronate solution of 120 mg/ml concentration has been observed at physiological temperature. It is shown that this temperature-dependent behavior can be related to the orientational polarizability term in the Debye theory of polar molecules in liquids.
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  • 6
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    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 945-964 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In 1974, Zimm described a theory which predicts that the sedimentation coefficient of high-molecular-weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed-dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well-defined sucrose-gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T-even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild-type phage (T4D+) was also used in some experiments.In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.The results show that in the range of 25,000-50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed-dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.
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  • 7
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fixation of cis (NH3)2Cl2Pt(II) to poly(I)·poly(C) leads to the formation of two complexed species. One involves coordination to a single base (accounting for about 70% of the total platinum bound over the rb range 0.07-0.25) and the other to two bases which are not adjacent to each other but may be on the same strand and separated by a loop. Reaction of the platinum compound with poly(I) gives in addition to the above two species a minor one (about 15%, independent of rb over the range 0.05-0.30) in which the platinum is bound to two adjacent bases. The availability of such coordination reduces the dominance of the 1:1 species, which, however, remains the major one (ca. 55%).
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  • 8
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    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1329-1344 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The complex of CH3Hg(II) with the accessible cysteines of glyceraldehyde-3-phosphate dehydrogenase (GAPD, EC 1.2.1.12) from rabbit muscle has been studied by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The wavelength dependence of the phosphorescence decay kinetics has also been measured. Comparison of CH3Hg(II)-GAPD with GAPD by these methods shows that a specific optically resolved tryptophan site of GAPD is perturbed by the interaction with a nearby mercury atom. The perturbation on the luminescence and ODMR properties is typical of an external heavy-atom effect. Based on the x-ray diffraction structure of the lobster enzyme, it is proposed that the heavy-atom effect results from the interaction of tryptophan-310 with CH3Hg(II) bound to cysteine-281 in the rabbit muscle enzyme.
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  • 9
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    Biopolymers 19 (1980), S. 1415-1434 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The energy of interaction of a spermine molecule with the A- and B-forms of DNA has been calculated, assuming that the molecule of spermine is fixed in the narrow groove of the DNA helix with the formation of hydrogen bonds between the amino groups of spermine and the phosphate groups of DNA. The atom-atom potentials method was used. Optimal structures for the A-DNA-spermine and B-DNA-spermine complexes are suggested. It is shown that, in agreement with the experimental data, the interaction of the spermine molecule with the A-DNA is energetically more favorable than that with the B-DNA. Two main factors are responsible for this: (1) the distance between neighboring phosphates of the chain in A-DNA (which is about 1 Å less than that in B-DNA) corresponds better to the distance between the amino groups of the propyl part of spermine; and (2) the orientation of phosphate groups in A-DNA inside the groove is preferable for complex formation with spermine to the outside groove arrangement of the phosphates in B-DNA. These conclusions are further confirmed by the calculations for DNA-propane diamine complexes.
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  • 10
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analog of valinomycin, cyclo[-(D-Ile-Lac-Ile-D-Hyi)3-] (C60H102N6O18), has been determined by x-ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds N—H…O=C, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso-valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L-Lac residues, the less crowded face.
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  • 11
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    Biopolymers 19 (1980), S. 1555-1566 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Possible conformations of lacto-N-tetraose, lacto-N-neotetraose, related disaccharides, and other milk oligosaccharides have been studied by an energy-minimization procedure using empirical potential functions. Lacto-N-tetraose favors a “curved” conformation, while lacto-N-neotetraose favors an approximately “straight” conformation. These two conformations differ mainly in the position of the terminal galactose residue with respect to the rest of the molecule. This difference explains the greater strength of lacto-N-neotetraose compared with lacto-N-tetraose in its ability to inhibit the cross-reaction of blood group P1 fractions with Type XIV pneumococcal antipolysaccharide. Although the favored conformation of lacto-N-tetraose (inactive) agrees with the model proposed by the earlier workers, that for lacto-N-neotetraose (active) differs. The favored conformations for the disaccharides galactose-β(1-4)-N-acetylglucosamine, galactose-β(1-3)-N-acetylglucosamine, and lactose are similar in overall shape, differing only in the nature and orientation of the side groups. This explains their nearly equal inhibitory activity. These theoretical models also explain the increased activity of lacto-N-fucopentaose I over that of lacto-N-tetraose and the relative activities of the substituted lactoses. The present studies suggest that it is the overall shape of the molecule which is important for activity, rather than the terminal β(1-4)-linked galactose residue alone.
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  • 12
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    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1571-1585 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C spin-lattice relaxation times of poly(L-lysine) have been obtained at 67.9 MHz in aqueous solution and in a mixed solvent (40% methanol/60% water). A concomitant determination of the conformation by CD permits the correlation of conformation and rotational diffusion of the polymer. The dependence on pH of the spin-lattice relaxation times of the 13Cα and the side-chain carbon resonances reflects the diffusional motion in the random-coil conformation, in the helix-coil transition, and in the conformation of the α-helix. In the mixed solvent the reorientational correlation time of the Cα-Hα vector increases from τ = 0.37 nsec (random coil) to τ = 12.0 nsec (α-helix). In aqueous solution the correlation time of this vector increases from τ = 0.33 nsec (random coil) to τ ≫ 11 nsec. The reorientation rates of the side-chain methylene groups in the two solvents are markedly different. The reorientation of all methylene groups is reduced in the mixed solvent.
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  • 13
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solid-state conformation of copolymers of β-benzyl-L-aspartate [L-Asp(OBzl)] with L-leucine (L-Leu), L-alanine (L-Ala), L-valine (L-Val), γ-benzyl-L-glutamate [L-Glu(OBzl)], or ∊-carbobenzoxy-L-lysine (Cbz-L-Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700-250 cm-1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L-Asp(OBzl)] induces a change from the left-handed into the right-handed α-helix. This conformational change for the poly[L-Asp(OBzl)] copolymers was observed in the following composition ranges: L-Leu, 0-15 mol %; L-Ala, 0-32 mol %; L-Val, 0-8 mol %; L-Glu(OBzl), 3-10 mol %; and Cbz-L-Lys, 0-9 mol %.
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  • 14
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    Biopolymers 19 (1980), S. 1667-1673 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dry purified ligamentum nuchae elastin has been investigated for physical aging. The samples were quenched from a temperature (197°C) close to the softening point to a number of measuring temperatures ranging from -20 to +180°C. At each temperature, the small-strain torsional creep properties were determined at a number of elapsed intervals after the quench. Aging effects were found over the whole temperature range, and the creep and aging behavior of elastin turned out to be very similar to that of synthetic polymers.
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  • 15
    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 19 (1980), S. 1705-1713 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Covalently closed circular DNA can exist in different configurations known as circular, toroidal, and interwound. Changes among these forms can be made in several ways, including the insertion of dye molecules between adjacent base pairs, which tends to untwist the double-helical structure. The aim of this paper is to discuss these configurations, and the changes among them, in the context of classical elastomechanics. The concepts of twisting, linkage and writhing are explained. Simple experiments on a twisted linear-elastic rod are described, and it is shown that although the circular and interwound forms may be modeled in this way, the toroidal form does not occur, being mechanically unstable. Theoretical energy calculations by Levitt on bent and twisted DNA show that DNA exhibits a particular kind of nonlinear elasticity in which there is an unusual coupling between bending and twisting. The aim of the paper is to show qualitatively that this special kind of elasticity can stabilize the toroidal form of closed circular DNA.
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  • 17
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    Biopolymers 19 (1980), S. 1357-1374 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light-scattering, viscosity, and sedimentation experiments on aqueous solutions of k-carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long-range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer-Fixman analysis, giving a value for the Mark-Houwink coefficient under theta-conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark-Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light-scattering radius. The relations between molecular parameters are corrected for the poly-dispersity of the sample.
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  • 18
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    Biopolymers 19 (1980), S. 1407-1414 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 19
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    Biopolymers 19 (1980) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 20
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    Biopolymers 19 (1980), S. 1475-1489 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An approximate analytic expression for the translational friction coefficient of a toroid modeled as a continuous shell of frictional elements is derived using the Kirkwood approximation. The accuracy of this expression was determined by comparing the friction coefficients predicted by it to those predicted by extrapolated shell-model calculations using the modified Oseen tensor. To show that these calculations do indeed yield the correct friction coefficients, actual translational friction coefficients were determined by observing settling rates of macroscopic model rings or toroids in a high-viscosity silicone fluid. Our conclusion is that the approximate expression yields friction coefficients that are about 1.5-3% low for finite rings. For thin rings, a comparison is also made with the exact result of Yamakawa and Yamaki [J. Chem. Phys. 57, 1572 (1972); 58, 2049 (1973)] for the translational friction of plane polygonal rings. This comparison shows that the approximate expression yields results which are low by 2-3% unless the rings are extremely thin, in which case the error is larger. In the limit of an infinitely thin ring the approximate expression reduces to the Kirkwood result [J. Polym. Sci. 12, 1 (1954)], which is low by 8.3%. We discuss briefly how this work may be useful in determining the structure of DNA compacted by various solvent-electrolyte systems and polyamines.
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  • 21
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    Biopolymers 19 (1980), S. 1451-1474 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Internal Brownian motions of clean φ29 and λ-DNAs have been studied using photon-correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm-2, can in every case be satisfactorily simulated by a Rouse-Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single-strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single-strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single-strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse-Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light-scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.
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  • 22
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    Biopolymers 19 (1980), S. 1507-1515 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman spectra of polyribouridylic acid excited in the uv region, from 363 to 290 nm, are reported. The conformational changes of the polymer from random coil to ordered structure with stacked bases at high and low temperature, respectively, are reflected by important changes in the Raman line intensities; this Raman hypochromism is itself a function of the excitation wavelength - its profile has been determined and shows negative values in the region of 290 nm (near resonance), i.e., hypochromism becomes hyperchromism. Thus the knowledge of the hypochromism excitation profile is important in following order-disorder transition of a polymer using resonance Raman spectroscopy. Theoretical attempts are proposed for explanation, involving not only the relative variations of the molar extinction coefficient on the order-disorder transition of the polymer, but also the damping factors of the vibronic levels. The theoretical curve is found to fit adequately the experimental data over the excitation range, using only the frequency of the O-O transition of uracil and a vibronic linewidth of 2200 cm-1.
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  • 23
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    Biopolymers 19 (1980), S. 2177-2190 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preferential interaction of sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) with the solvent components in water/2-chloroethanol mixtures has been determined using density-increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2-chloroethanol and at constant chemical potential of 2-chloroethanol. Sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2-chloroethanol-induced coil-to-helix transition of sodium poly(α-L-glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α-L-glutamate) is solvated by one 2-chloroethanol molecule. The location of water and 2-chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.
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  • 24
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    Biopolymers 19 (1980), S. 2223-2245 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complex formation between tryptamine and mononucleotides and dinucleoside phosphates containing adenine and/or cytosine has been studied at five pD's ranging from 1.1 to 7.4 by proton magnetic resonance spectroscopy. Chemical shifts of base ring protons and the ribose anomeric proton in the nucleotides and indole ring protons in tryptamine were monitored and their changes with pD and intermolecular interactions interpreted qualitatively. Stacked complexes were found to exist at all pD's in the range studied. Complex geometries differ depending on pD. An electrostatic interaction between the tryptamine amino group and the nucleotide phosphate group contributes to complex formation above pD 4 but is not strong enough to shift the dinucleoside phosphate equilibrium towards the unstacked conformer.
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  • 25
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical conformational energy calculations have been carried out for N-methyl derivatives of alanine and phenylalanine dipeptide models and N-methyl-substituted active analogs of three biologically active peptides, namely thyrotropin-releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone-releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N-methylated residue is in the trans configuration show that (1) N-methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around φ = -135° ± 5° and ψ = 75° ± 5°, and (3) the αL conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C5 (extended) conformation is second lowest in energy. When the peptide bond (ωi) is in the cis configuration the ith residue is energetically forbidden in the range φ = 0° to 180° and ψ = -180° to +180°. Conformations of low energy for ωi = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the αR conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low-energy conformers are found for [(N-Me)His2]TRH. These conformers differ only in the φ and ψ values at the (N-Me)His2 residue. Among the different low-energy conformers found for each of the ENK analogs [D-Ala2,(N-Me)Phe4, Met5]ENK amide and [D-Ala2,(N-Me)Met5]ENK amide, one low-energy conformer was found to be common for both analogs with respect to the side-chain orientations. The stability of the low-energy structures is discussed in the light of the activity of other analogs. Two low-energy conformers were found for [(N-Me)Leu7]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D-Ala6,(M-Me)Leu7]LHRH is considered.
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  • 26
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Based on steric and electrostatic considerations, the prerequisites for binding to DNA via the intercalation mechanism are proposed. Steric contour energy curves are presented to demonstrate the region inaccessible to an intercalant. They are calculated with a 6-n (n = 14) potential. This method is a soft potential analog of an excluded-volume approach. Electrostatic contours on the steric surface illustrate the relatively positive and negative regions of the binding site. The principal intercalation sites, predicted to fit into B-DNA via a tetramer-duplex unit, and the unconstrained dimer-duplex units, obtained in crystal structures, are examined. These contours illustrate the requirements of size, conformation, and net atomic charges necessary for intercalation and optimum binding. Based on the limited space available for intercalation by the presence of the backbone and the maximum base-pair separation of 8.25 Å, an Essential Metabolite Exclusion Hypothesis is presented.
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  • 27
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the near-uv CD spectrum of lysozyme was carried out in the presence and absence of the inhibitor tri-N-acetylglucosamine, and theoretical chiroptical calculations based on the tetragonal crystal structure of the enzyme and the enzyme-inhibitor complex were performed. The results of these calculations indicate that the near-uv CD spectrum of lysozyme can be adequately explained in terms of negative rotatory strengths arising from the tryptophan 1La (293-300 nm) and the disulfide n-σ* bands (250 rm), and positive rotatory strength contributions from the tryptophan 1Lb bands (291 nm) and the tyrosine 1Lb bands (275 nm). Contributions to the rotatory strength of each band were approximated in terms of specific interactions between chromophores. It was found that the rotatory strength of most of the near-uv transitions arises primarily from coupling interactions involving other side-chain chromophores and amide groups which are in close proximity. Changes which are observed in the lysozyme CD spectrum on binding of tri-N-acetylglucosamine may be explained in terms of changes in the rotatory strength which result from interactions of the 1La transitions of the active-site tryptophans with the acetamide groups of the inhibitor. The reasonable agreement which is found between the experimental and calculated rotatory strengths implies that the crystal conformation of lysozyme must resemble the solution conformation.
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  • 28
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of the following oligo- and co-oligopeptides by the liquid-phase method is described: (L-Met)15 (I), [L-Glu(OBzl)]20 (II), (L-Val)8-Gly (IV), (L-Ile)8-Gly (V), (L-Ile)4-Gly-(L-Ile)4 (VI), (L-Ile)4-Pro-(L-Ile)4 (VII), (L-Met)5-L-Pro-(L-Met)5 (VIII), [L-Glu(OBzl)]7-L-Pro-[L-Glu(OBzl)]7 (IX). The oligomers are covalently bound to bifunctional polyethylene glycol (PEG) and monofunctional PEG-M of Mr 5 × 103-2 × 104. Analytical controls were carried out after each step of synthesis in order to ensure quantitative coupling yields. All products could be obtained in high purity as indicated by amino acid analysis, thin-layer chromatography and chiroptical methods. The solubility of the oligomers was strongly enhanced by the presence of the C-terminal PEG group, enabling conformational investigations in a variety of solvents. A significant relationship between conformation and physicochemical properties of the oligopeptides was observed. Oligomers with tendencies to adopt α-helical (I, II) or unordered structures (VI-IX) showed no pronounced change in solubility or coupling kinetics during chain elongation, whereas the onset of a β-structure (IV, V) was paralleled by a drastic decrease in solubility and reactivity of the terminal amino groups. Most notably, the insertion of a proline or glycine in the middle of a β-forming peptide chain (VI, VII) resulted in a considerable increase in solubility compared to the corresponding homo-oligomers. The impact of the conformational properties of a peptide chain on strategic considerations of peptide synthesis in solution is delineated.
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  • 29
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational analysis of the CD spectrum is reported for the synthetic and membrane-modifying nonadecapeptide analog of alamethicin N-t-Boc-(Aib-L-Ala)5-Gly-Ala-Aib-Pro-Ala-Aib-Aib-Glu(OBzl)- Gln-OMe. The CD data are evaluated according to three different methods and are discussed with respect to those obtained from natural alamethicin and suitable models such as N-t-Boc-(Aib-L-Ala)7-OPOE, fragments of the synthetic nonadecapeptide, and the hexadecapeptide N-t-Boc-(Aib-L-Ala)5-Pro-Ala-Aib-Aib-Glu(OBzl)-Gln-OMe. The synthetic nonadecapeptide with the longer helical region exhibits membrane activities comparable to those of alamethicin, whereas the hexadecapeptide with the shorter helix is inactive.
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  • 30
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    Biopolymers 19 (1980) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 31
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    Biopolymers 19 (1980), S. 231-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper deals with the light scattering from particles rotating in a flow with a transverse velocity gradient. It is theoretically substantiated and experimentally proved that the scattered light spectrum contains reliable information of the particle configuration and dimensions. The proposed technique may prove also very promising for the analysis of particle polydispersion.
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  • 32
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of poly(ε-L-lysine) is described. This is a poly(ε-amino acid) in which the ε-amino group of lysine is condensed with the α-carboxyl group to produce a chain backbone that is a variant of the usual one seen in proteins and the side chain is the α-amino group. Conformational studies of poly(ε-L-lysine) and its t-butyloxycarbonyl derivative suggest the likelihood of a chain order that is formally similar to the antiparallel pleated-sheet conformation of proteins.
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  • 33
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied the kinetics of oscillatory tensile forces in collagen membranes. These forces were generated by sinusoidal electric fields applied across the membrane. Both the magnitude and phase of the measured force changed with frequency over a three-decade range. The membrane-separated electrolyte baths had different ionic strength but identical non-isoelectric pH. Changes in intramembrane ionic strength due to the electric field were calculated over the same frequency range via an electrodiffusion model that was generalized to include convection and electrokinetic coupling. A comparison of the experimental and theoretical phases and amplitudes versus frequency suggests that electrodiffusion is the dominant rate-limiting process in this electromechanochemical transduction. These results are relevant to electrostatic interactions in connective tissues and to membrane-based filtration devices in which membrane permeability may be actively varied and controlled by an applied electric field.
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  • 34
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    Biopolymers 19 (1980), S. 263-272 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Integral enthalpies of solution of several dipeptides and tripeptides in water at low concentrations have been determined at 25 and 35°C. These data have been used to derive the changes in heat capacity on dissolution at infinite dilution ΔCp0 at 30°C. Limiting partial molal heat capacities ΔCp20 have been determined by combining ΔCp0 with Cp2 (heat capacity of pure solid peptides). Using the data on ω-amino acids and these peptides, the partial molal heat capacity of a peptide group —CONH— was semiquantitatively estimated.
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  • 35
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    Biopolymers 19 (1980), S. 273-284 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Integral enthalpies of solution at low concentrations of several amino acids and peptides in 2 and 6M urea solutions have been determined at 25 and 35°C. These data have been used to derive the enthalpies of transfer (at 25 and 35°C) and heat capacities of transfer (at 30°C) of these amino acids and peptides from water to aqueous urea solutions. Furthermore, the enthalpies of transfer and heat capacities of transfer per CH2 group and per peptide group —CONH— have also been estimated. These results show that while the enthalpies and heat capacities of transfer per CH2 group are positive and negative, respectively, the reverse is true for —CONH— group. The implications of these results in the mechanism of the denaturation of proteins by urea are discussed.
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  • 36
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectra of cUpUp, cCpCp, and cGpGp derived from DCC-catalyzed polymerization of the relevant protected ribonucleoside 3′-phosphates are described. Similar studies on Up, U 〉 p, and cUp, as well as cUpUpUp and cUpUpUpUp, are presented. The spectral properties of the cyclic oligomers are compared with those of the corresponding linear oligomers with terminal 3′-phosphates so as to demonstrate that disruption of normal right-handed base stacking is considerable in these RNA loops.
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  • 37
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    Biopolymers 19 (1980), S. 297-309 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The polymerization of 1,2-anhydro-3,4,6-tri-O-benzyl-β-D-mannopyranose proceeds in the presence of Lewis acids, cationic coordination catalysts, and strong bases. Debenzylation of the products yields oligomeric saccharides or low polymers. Polymerization in toluene by means of potassium alkoxide complexed with crown ethers leads to essentially stereoregular (1 → 2)-α-D-mannopyranan. The original derivatives have been characterized by optical rotation, viscosity, molecular weight, gel permeation chromatography, and spectrometry. The free polysaccharides have been characterized by optical rotation, molecular weight, and 1H- and 13C-nmr spectrometry and compared to yeast mannan hydrolysate oligomers.
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  • 38
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH3+ prototype test probe with B-form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH3+-like ion interacting with (G-C)4, (A-T)4, and [(G-C)·(A-T)]2 deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH3+-like ion is near known alkylation sites. The results of the Az+ … [(G-C)·(A-T)]2 interaction are virtually identical to those found for the CH3+-like ion. Aqueous solvation energetics have little effect on the physical association of Az+ with [(G-C)·(A-T)]2.
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  • 39
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    Biopolymers 19 (1980), S. 325-340 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of molecular orbital calculations, using MINDO/3 and CNDO/2L methods, have been used to characterize the chemical reaction of protonated aziridine with DNA nucleophilic base sites. The N-7 atom of guanine is found to be the preferred alkylation site only when the O-6 atom of guanine is involved in base-pair hydrogen bonding. Otherwise O-6 is the predicted major site of alkylation. This indirectly suggests that protonated aziridine alkylation processes involve base-paired DNA structures, since N-7 guanine is the observed major site of alkylation. Alkylation of N-3 adenine is predicted to be more favorable than chemical attack of the N-7 adenine position. Both of these sites, however, are predicted to be less reactive than N-7 of guanine. These chemical reactivity studies resolve alkylation specifically not achieved in the DNA-alkylator physical association calculations reported in the preceding paper.
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  • 40
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    Biopolymers 19 (1980), S. 341-352 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Infrared dichroic studies and deuterium exchange measurements of somatostatin and some of its analogs incorporated in uniaxially oriented polyoxyethylene are described. Band positions and dichroic ratios in the N-H stretching and amide I and II regions are similar to those of flexible and nonordered peptides like valinomycin and poly[Glu(ONa)]. This information, together with fast deuterium exchange rates, suggests that somatostatin exists in a flexible nonordered conformation in polyoxyethylene. One analog, di-S3,14-acetamidomethyl dihydrosomatostatin, was found to exist in both nonordered and β-like conformations.
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  • 41
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    Biopolymers 19 (1980), S. 395-418 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Monte Carlo simulation of the structure of the 16 ordered and disordered waters in the unit cell of crystals of the cyclic peptide cyclo(-L-Ala-L-Pro-D-Phe)2 is reported. The water structure has been characterized in terms of the statistically averaged positions of the individual molecules, their root-mean-square movements about these positions, the probability of finding a water in a given spatial position in the crystal (probability maps), and examination of individual configurations of the system. In this way a picture is obtained of the water structure, including water orientations (hydrogen positions), the hydrogen-bonding network, and fluctuations in these structural features, to a degree hitherto unavailable either from experimental or theoretical studies. In addition, the variation in water structure in various peptide environments was studied and correlated with the energetics of the individual water molecules. Variations in the crystalline environment of different water molecules lead to energy differences of as much as 4-5 kcal/mol in their average energies. Similarly, differences are observed in the water-peptide and water-water components of the energy. Two different water potentials were tested. The results were compared with experimental data in terms of mean positions, root-mean-square movements, and the Fourier transform of the simulated water structure. The agreement factor (R factor) calculated from the theoretical water probability distribution was 18.8% compared to the x-ray value of 14.5%, and the value of 28% when the water is omitted.
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  • 42
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    Biopolymers 19 (1980) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 43
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    Biopolymers 19 (1980), S. 445-448 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 44
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational energy calculations on the N-acetyl-N′-methylamides of dehydroalanine and N-methyldehydroalanine indicate that their conformational behavior is very different from that of the corresponding saturated compounds. The conformational data in the literature from x-ray and nmr investigations on peptides containing α,β-unsaturated residues are discussed on the basis of these theoretical results.
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  • 45
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    Biopolymers 19 (1980), S. 493-507 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amphipatic block copolymers (OβEb) with a hydrophilic saccharide block and a hydrophobic polypeptide block were synthesized. In these copolymers the saccharide block is the glyco-amino acid Oβ from ovomucoid and the peptide block (Eb) is a poly(γ-benzyl-L-glutamate) block. Copolymers OβEb exhibit, in the solid state and in Me2SO concentrated solutions, mesomorphic lamellar structures where the polypeptide chains are in an α-helical conformation. Depending on the molecular weight of the polypeptide block, three types of lamellar structures are obtained, and they differ by the mode of organization of the polypeptide chains in their lamellae and by the T or Y conformation of the saccharide block.
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  • 46
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formation of complex between the Cu2+ ion and poly(α-L-glutamic acid) [poly(Glu)] in 150 mM NaCl solutions was studied by uv-visible absorption and equilibrium dialysis methods at the mixing ratios of Glu residues to Cu2+, R, of 32, 16, and 8 and in the pH range 4-7. The results showed that more than 90% of Cu2+ ions bind to the poly(Glu) at pH 〉 4.9, but the bound Cu(II) begins to dissociate with a decrease in pH. The absorption spectra of bound Cu(II) varied with pH and R in a complicated manner. Three different component spectra were disclosed from the analysis of the pH dependence of the bound spectra. We concluded that poly(Glu)-Cu(II) complexes fall into three classes in the pH range 4-7, with the proportions of these complexes varying with both pH and R. The three complexes predominate either in the helix or extended-coil region, in the helix-coil transition region, or in the helix-aggregate region. The stability constant and binding mode of each Cu(II)-Glu complex were estimated from the dialysis data. With these results, the possible structure of each complex is discussed.
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  • 47
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The variable-temperature proton nmr spectra of the oligoribonucleotides in the series CpApX and the series ApGpX, X = A, G, C, U, together with the parent dimers CpA and ApG have been measured. A complete analysis of all the nonexchangeable base proton resonances and ribose H-1′ proton resonances was made. The presence of trends in the shielding abilities of the various bases at both the nearest-neighbor and next-nearest-neighbor positions were identified. The observed shieldings could be used to predict the chemical shifts of protons in related systems. Based on the empirical results from ribodinucleoside monophosphates, the temperature-dependent behavior of the J1′2′ coupling constants of the triribonucleotides suggested that the compounds in the CpApX series stacked from the 5′-end to the 3′-end, while those in the ApGpX series stacked from the 3′-end to the 5′-end.
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  • 48
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    Biopolymers 19 (1980), S. 619-637 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Closed random Gaussian polygonal chains of N (6 〈 N 〈 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types - 0, 31, 41, 51, and 52 - the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw2/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N1/4 (w/N)2, and therefore depends on the writhing density and on the length of the DNA.
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  • 49
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    Biopolymers 19 (1980), S. 575-595 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A band-centrifugation method for the analysis of an assembly reaction of a simple virus from its RNA and protein is described. The experiment was carried out by sedimenting a band of viral RNA through a solution of depolymerized coat protein. The resulting radial distribution of the reaction products, followed as a function of time, was analyzed by a computer simulation of the series of reaction. This method is based on a numerical solution of the continuity equation for the sedimentation-diffusion process [Claverie, J.-M., Dreux, H. & Cohen, R. (1975) Biopolymers 14, 1685-1700; Cohen, R. & Claverie, J.-M. (1975) Biopolymers 14, 1701-1716]. A numerical method for the simulation of the chemical reaction is derived. From the simulated reaction series, equilibrium constants emerge for the successive addition of protein subunits to the growing nucleoprotein particle.The method is applied to the assembly of alfalfa mosaic virus. If the reaction between RNA and protein is carried out in 0.32M CsCl, pH 7.0, two stages during particle growth are resolved, each characterized by an equilibrium constant K. The determined values for K range from 5 × 105 to 3 × 106 l. mol-1. The existence of these two stages may have a structural implication in the assembly, as they likely represent an elongation and a termination stage. If the reaction is carried out under more favorable conditions (0.25M CsCl, pH 7.0), a kinetic constant of at least 105 l. mol-1 sec-1 is derived for each reaction step. Under these conditions the assembly appears to be completed within 1 min, which is too fast to detect distinct stages by band sedimentation.
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    Biopolymers 19 (1980), S. 597-617 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Purified insoluble elastin samples labeled with [1-13C]valine, [1-13C]alanine, and [1-13C]-lysine were prepared from chick aorta in culture. The molecular mobility at the labeled sites was investigated using 13C-1H magnetic double-resonance spectroscopy. Linewidths, T1, and nuclear Overhauser effect (NOE) values of the labeled carbons alone were obtained from dipolar decoupled difference spectra. Analysis of these parameters together with signal intensity measurements showed that essentially all the valyl residues, ca. 75% of the alanyl residues, and ca. 60% of the lysyl residues were characterized by rapid backbone motions having τ = 65 nsec. Resonances due to the remaining alanyl and lysyl residues were detected in cross-polarization experiments, which enhance the signals of motionally restricted carbons. Since lysyl and alanyl residues are found in the crosslink regions of elastin, whereas valyl residues are not, we conclude that crosslinks rather than secondary structures in the extensible region of the protein are the main source of motional restrictions in the protein. Elastin chain mobility was monitored by linewidth measurements over the range -90 to +70°C. When the swelling solvent (0.15M NaCl) was fixed at 0.6 g/g of elastin, a rapid monotonic reduction in chain mobility was observed as the temperature was lowered from 50 to 5°C. Liquidlike mobility was completely lost at 5°C. In contrast, the same sample in contact with excess solvent retained its liquidlike molecular mobility until -13°C, where it abruptly became rigid. The molecular mobility of this sample was temperature insensitive in the physiologically interesting range, 20-40°C, as a consequence of the opposing influences of temperature and swelling. Taken together these nmr data indicate that under physiological conditions, elastin is a network of mobile chains whose motions are strongly influenced by protein-solvent interactions.
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    Biopolymers 19 (1980), S. 639-653 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preferential solvation of the glucans amylose, pullulan, and dextran in binary dimethyl-sulfoxide/water (DMSO/H2O) solvent mixtures has been measured using gel-permeation chromatography. The preferential solvation behavior of the three glucans in DMSO/H2O solvent mixtures is indistinguishable in the experiments reported. In solvent mixtures with mol ratio DMSO/H2O less than 1:2, all three glucans are solvated preferentially by H2O. The maximum extent of preferential solvation by H2O is about 2.5 mol H2O/mol of glucose residues. When the DMSO/H2O mol ratio exceeds 1:2, DMSO solvates the glucans preferentially to a maximum extent of about 1 mol DMSO/mol of glucose residues. An interpretation of the change in preferential solvation with mixed solvent composition is suggested in terms of the known characteristics of the binary solvent system, and the relationship of preferential solvation, reported here, to the absolute solvation of the glucan chains is discussed.
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    Biopolymers 19 (1980), S. 669-679 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dc electrical conductivity of large single crystals of hen egg-white lysozyme has been measured. The samples were grown from aqueous solution and dried in air with silica gel. The temperature dependence of the conductivity obeyed the relation σ = σ0 exp(- ΔE/kT), with ΔE = 1.2 eV. The ΔE value agreed with most of the previous results for various proteins in the form of lyophilized powder. On the other hand, log σ0, being between 7 and 11, was much larger than the previously reported values and differed among the samples. An irreversible decrease in σ0, without affecting ΔE, was observed on heating the samples above 85°C. It was shown that the set of results can be explained if the charge carriers responsible for the observed conduction are regarded as protons, originating from residual water molecules. Photoresponse of the samples to uv radiation below 305-315 nm was also observed. Reproducible and reliable results were obtained relatively easily in the present experiments, which is thought to be the main advantage of using single-crystalline samples.
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    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 54
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    Biopolymers 22 (1983), S. 15-25 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long-range interactions between different regions, incorporating all these interactions in a single Ising-like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α- and β-structures for different residues in synthetic polypeptides, while long-range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x-ray structural data became available.
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    Biopolymers 22 (1983), S. 27-31 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To increase our understanding of peptide-water interactions, we are simulating the behavior of water molecules in the intermolecular channels of [Phe4Val6]antamanide dododecahydrate crystals. There is good overall agreement between the positions predicted using two alternative potential functions and those that have been observed by x-ray diffraction. Detailed differences between the predictions for the two potential functions are discussed.
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    Biopolymers 22 (1983), S. 49-58 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
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    Biopolymers 22 (1983), S. 87-91 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Near- and far-uv CD spectra of microtubule protein preparations have been examined to study the possible role of protein conformation in relation to the kinetics of the self-assembly of these proteins into microtubules in vitro. Although tubulin can form conformations with high helical content under apolar solution conditions, this transformation is apparently not involved in self-assembly. There is no major perturbation of tubulin near-uv CD by reagents and solution conditions favoring assembly. Thus, in these preparations, tubulin, as dimer and as oligomer with MAPs, is effectively in the conformation in which it undergoes self-assembly. This conclusion is consistent with a hybrid model of assembly of microtubule protein involving direct incorporation of oligomeric species as an alternative to the condensation polymerization of tubulin dimer as the exclusive assembly mechanism.
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    Biopolymers 22 (1983), S. 101-105 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ligand-modulated kinetics of the autoproteolysis of thermolysin and the high-molecular-weight products of the reaction provide evidence for the conclusion that separation of the two structural domains is most probably the first step on the unfolding pathway of the protein under native conditions.
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    Biopolymers 22 (1983), S. 125-129 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The in vivo pathway of folding and subunit assembly of a trimeric bacteriophage protein has been studied by characterizing precursors to the native protein and by analyzing temperature-sensitive mutations that kinetically block the pathway. The native trimer is formed via an intermediate composed of three partially folded chains, the protrimer. At 39°C, temperature-sensitive mutations prevent the formation of both the native trimer and the protrimer, possibly by destabilizing earlier intermediates. However, the mutations do not affect the stability of the native protein, formed at 30°C. Thus, these mutations identify amino acid residues involved in interactions that determine the folding pathway.
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    Biopolymers 19 (1980), S. 751-766 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general formalism, which includes translation-rotation coupling, is proposed for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape. This formalism is based on Brenner's theory of translational-rotational dynamics and on methods for the calculation of hydrodynamic properties that have been already presented, and can be regarded as a generalization of the one proposed by Nakajima and Wada. The calculated transport properties depend on the origin as predicted by Brenner's theory, but in a disagreement with him, the center of resistance and the center of diffusion do not coincide. As one can define several hydrodynamic centers, which in practice turn out to be located at different points, the influence of the choice of the center on the calculated transport properties is discussed. An analysis of the translation-rotation coupling effects in translational diffusion reveals that they arise exclusively from hydrodynamic interactions and are rather small in some cases of interest. Finally, we present a study of the rotational diffusion of rigid bent rods with a fixed length-to-diameter ratio. The diffusion coefficients obtained can be useful to estimate changes with respect to a straight rod.
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    Biopolymers 22 (1983), S. 1677-1696 
    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 O2 release by oxyhemoglobin caused by sodium dithionite, in the presence and in the absence of organic cosolvents (monohydric alcohols and formamide) at 10°C. This study was performed by using standard stopped-flow techniques coupled with microprocessor-based data acquisition. We have fitted the experimental data to a mathematical expression obtained on the basis of a two-state model that takes into account the kinetic heterogeneity between α- and β-chains and the presence of αβ-dimers in oxyhemoglobin solutions. Results indicate that the cosolvents mainly affect the allosteric parameter L, i.e., the T ⇄ R conformational equilibrium of hemoglobin, leaving the intrinsic deoxygenation rates of both R and T states almost unaltered. The L values obtained in the present work are in excellent agreement with analogous values previously estimated from oxygen equilibrium measurements.
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    Biopolymers 22 (1983), S. 1657-1675 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Porcine submaxillary mucin (PSM) is a glycoprotein composed of a protein core and frequent, short oligosaccharide side chains. We report static and dynamic light scattering experiments and intrinsic viscosities for PSM in aqueous solvent systems. In 0.1M NaCl solution, the data suggest PSM exists as large, internally branched, highly hydrated, polydisperse aggregates that slowly dissociate to give a stable species of weight-average molecular weight (Mw) 7.4 × 106. In 6M GdnHCl solution, the noncovalent bonds between PSM molecules are broken, giving a highly elongated molecule of Mw = 2.0 × 106. The irreversible nature of this dissociation suggests that the forces that stabilize the native aggregates of PSM in 0.1M NaCl are specific in nature. On reduction of PSM with mercaptoethanol, the polydispersity decreases and Mw also decreases to 9 × 105. A discrete change is observed in the solution properties of PSM in 0.1M NaCl at a concentration of 2mg/mL, manifested by a sudden decrease in the translational diffusion coefficient, an increase in viscosity number, and a decrease in slope of the osmotic compressibility. We tentatively propose that a weak and reversible secondary association process occurs at this concentration, although a purely hydrodynamic interaction cannot be ruled out.
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  • 63
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    Topics: Chemistry and Pharmacology
    Notes: The uv linear dichroism of calf thylus DNA has been studied at different degrees of orientation both in flow-oriented ethanol-water solutions and in a stretched aqueous host of poly(vinyl alcohol) (PVA). The reduced dichroism (LDR) curves in the region 250-290 nm for DNA in PVA films at 75 and 100% relative humidity (r.h.) are in fair agreement with the curves calculated for the A- and B-forms of DNA, based on the fiber structures and the π-π* transitions of the free bases. This suggests that DNA adopts its A and B conformations in PVA at 75 and 100% r.h. In ethanol, on the other hand, a deviation from the A-form spectrum shows that the conformation of DNA in the solution can differ from the fiber structure. At shorter wavelenghts, a positive contribution to LDR is explained in terms of an out-of-plane polarized n-π* transition.
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    Biopolymers 22 (1983), S. 1759-1767 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A vibrational analysis has been performed for a double-helix-single-strand junction. A Green's function technique has been used in treating the junction as a defect on an otherwise perfect system of infinite chain homopolymers. We calculate that the hydrogen-bond stretching at the junction is amplified by a factor of two relative to the interior of the double helix, B poly(dG)-poly(dC). Breathing modes localized near the junction have also been predicted at 77 and 94 wave numbers. The calculated results are shown to be consistent with predictions from recent nmr studies.
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    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 66
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    Topics: Chemistry and Pharmacology
    Notes: Nmr studies of the protected and free tetrapeptide Gly-Pro-Gly-Gly were carried out in β-turn-supporting solvents, that is, in CDCl3 for Z-Gly-Pro-Gly-Gly-OMe and in Me2SO-d6 for H-Gly-Pro-Gly-Gly-OH. Comparisons with specifically α-deuterated analogs gave complete assignments of the NH and methylene regions. Analysis of chemical shifts, coupling constants, and the temperature dependence of chemical shifts show that the peptide adopts a type II β-turn conformation. This turn is stabilized for the protected tetrapeptide by two hydrogen bonds between (i) C=O (Gly1) and NH(Gly4), and (ii) urethane function NH and methyl ester C=O.
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  • 67
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    Topics: Chemistry and Pharmacology
    Notes: Ab initio minimal and split-valence basis set calculations have been performed on compounds that are involved in retro-inverso modifications, i.e., gem-diaminoalkyl and malonyl structures. These calculations are compared with empirical force field calculations and the minor differences discussed. All calculations agree that the preferred helical conformation of the isolated gem-diaminoalkyl and malonyl derivatives of residues found in the retro-inverso modified peptides is 5-8 kcal/mol lower than the Ceq7 conformation preferred by the isolated peptide residues. Population analysis and contour plots of the charge distribution are used to help explain the differences between the model compounds.
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    Biopolymers 22 (1983) 
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    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 22 (1983), S. 1449-1460 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: SCF-LCAO-MO ab initio calculations were carried out for the interaction between a charged amino acid and a water molecule. The results obtained were fitted by an analytical potential function of the atom-atom type, and the corresponding potential surfaces were examined by means of orientationally optimized isoenergy contour maps. Monte Carlo simulations were also carried out on a few selected solute-water clusters at T = 300 K, in order to obtain insight into the solvation structure.
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  • 71
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    Topics: Chemistry and Pharmacology
    Notes: An improved cube method has been developed for calculating the intensity of diffuse x-ray scattering of macromolecules in solution using a certain set of their atomic coordinates. The technique is based on the ideas of B. Lee and F. M. Richards [(1971) J. Mol. Biol. 55, 374-400] and Richards [(1977) Annu. Rev. Biophys. Bioeng. 6, 151-176] on the possibility of estimating the molecular and accessible surface of a particle by “rolling” a sphere, simulating a water molecule, on its molecular surface. It is shown that this technique is more advantageous than earlier versions of the cube methods. The improved technique for calculating scattering curves was utilized for several globular proteins, and for the first time, reliable scattering curves were obtained for protein-“bound” water complexes. In the case of globular proteins and tRNA, this technique has permitted a strict evaluation of their accessible surfaces, their volumes, and, apparently for the first time, their complete molecular surfaces.
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    Biopolymers 22 (1983) 
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    Biopolymers 22 (1983), S. 2501-2506 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 22 (1983), S. 2523-2538 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extended retro-inverso modification was introduced at the central six residues of the somatostatin molecule, the region of internal enzymatic degradations. The synthesis of the analog [Ala4,g-Phe6-r-D-Phe7-r-D-Trp8-r-D-Lys9-r-D-Thr10-m-R,S-Phe11]-somatostatin required a unique strategy accommodating the unusual structure. Side-chain protection based on the t-butyl group in combination with Fmoc and Nps α-amino protection was employed. The key component containing the gem-diaminoalkyl residue was generated by an iodobenzene bistrifluoroacetate-mediated reaction. The separation of diastereomers of the cyclic tetradecapeptide in highly pure form was accomplished by high-performance liguid chromatography on a semipreparative scale. The analogs exhibited very low potency in the growth hormone inhibition test in vitro. This is interpreted as the consequence of the complex structural changes created by the extended retro-inverso modification.
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  • 75
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    Topics: Chemistry and Pharmacology
    Notes: The nature of internal and overall motions in native (double-stranded) and denatured (single-stranded) DNA fragments 120-160 base pairs (bp) long is examined by molecular-dynamics modeling using 13C-nmr spin-relaxation data obtained over the frequency range of 37-125 MHz. The broad range of 13C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T1 values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double-stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τx = ∼10-6 s;τZ = ∼1.8 × 10-8s), which is in good agreement with values calculated from hydrodynamic theory (τx = ∼1.8 × 10-6 s; τZ = ∼2.7 × 10-8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual C—H vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τw = ∼4 × 10-9 s, θcone = ∼21°) or as a bistable jump (τA = τB = ∼2 × 10-9 s, θ = ∼15°). We discuss the critical role in molecular-dynamics modeling played by the angle (β) that individual C—H vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τW = ∼0.2 × 10-9 s, θcone = ∼50°), and overall motion is affected by becoming essentially isotropic (τx = τZ = ∼5 × 10-8 s) for the single-stranded molecules. Since 13C-nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.
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  • 76
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    Topics: Chemistry and Pharmacology
    Notes: The interaction of methyl orange with poly(L-lysine) was studied kinetically by the stopped-flow technique with CD detection, as well as by static CD titration experiments. In the static experiments, the differences observed in the polymer-to-dye ratio dependences of the CD spectra and absorption spectra suggested at least two kinds of bound states of the methyl orange attached to the polymer. The kinetic experiments using the stopped-flow apparatus, however, revealed four distinct reaction processes. The reaction mechanism was elucidated from the concentration dependence of the time constant for each process as follows: the first process was attributed to the bimolecular binding step of methyl orange to the side chain of poly(L-lysine), the second and third process were ascribed to the intramolecular reaction of the polymer-dye complex, and the fourth process was found to be the intermolecular aggregation of the polymer-dye complex. The origin of the stacking of methyl orange on poly(L-lysine) is discussed on the basis of the characteristics of signal amplitudes obtained from the kinetic experiments for these processes.
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  • 77
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    Topics: Chemistry and Pharmacology
    Notes: Novel devices for the spectroscopic and chromatographic analysis of the denaturation curves of the protein are described. A multidimensional spectroscopic measuring system makes it possible to carry out simultaneous and continuous acquisition of a set of data of different spectroscopic dimensions at several wavelengths in the course of increasing or decreasing denaturational perturbation. GuHCl-gradient chromatography can provide information about the progressive change of the protein volume in the course of increasing GuHCl concentration. Thus, denaturation curves with a high data-point density can be obtained. The data-storing function by a magnetic disk memory provides enough precision for a rigorous investigation of the correlation among the curves that probe different aspects of denaturation. The GuHCl denaturation of RNase A, cytochrome c, and pepsinogen are studied to demonstrate the high performance of these devices. Three types of transitions are found in these three proteins and the multiphasic nature of the transitions is clearly detected in the last two proteins.
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    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 22 (1983), S. 2169-2172 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 22 (1983), S. 2207-2217 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A sufficiently long semiflexible filamentous macromolecule is theroretically expected to exhibit three different domains of behavior of its apparent diffusion coefficient Dapp(K) as a function of scattering vector K: (1) the small wave vector limit, where Dapp(K) = D0 is the translational diffusion coefficient of the center-of-mass; (2) the universal K3 region, where Dapp(K) = (kBT/6πη)K is a universal function of K independent of any property of the molecule itself; (c) the plateau region at large K2, where Dapp(K) approaches either a plateau, or gradually sloping quasiplateau, characteristic of local (elastic) rigid-body motions of the filament. The existence of each of these different domains has now been established experimentally for at least some polymers. The boundaries of the universal K3 region and the plateau region are determined theoretically here using precise quantitative criteria for universal or plateau behavior of Dapp(K) for a Rouse-Zimm model containing N + 1 subchains with rms subchain extension b. Allowing a maximum of 13% nonuniversal behavior, the domain of the universal K3 region is given by K2R2G = K2Nb2/6 ≥ 7 and K2b2 ≤ 0.54. Allowing as much as 10% nonplateau behavior, the boundary for onset of plateau behavior is K2b2 = 18.3. Dapp(K) is at least 50% nonuniversal when K2b2/6 = 6 ln 3. Extension of these results to DNA is examined theoretically, and good agreement of the pertinent predictions with published experimental data is demonstrated.It is concluded that no truly universal K3 region exists for DNA with Mr ≤ 107 and persistence length a ≥ 450 Å, although marginally (≤17% nonuniversal) universal behavior, is exhibited in a very narrow domain 0.64 × 1010 ≤ K2 ≤ 0.84 × 1010 cm-2 for φ29 DNA (Mr = 11.5 × 106). More than 50% of Dapp(K) is governed by local (elastic) rigid-body motions when K2 = 5.23 × 1010 cm-2. The existence of a very wide region of nonuniversal apparent K3 behavior extending up to very large K2, far into the plateau region, is demonstrated in a plot of Dapp(K)/K vs K2 for the Rouse-Zimm model. This is shown to stem in part from visual artifacts of plotting Dapp(K)/K vs K2, even for rigid species.
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 22 (1983), S. 2353-2366 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rotational relaxation tiem τ3 of DNA molecules (Mw ≃ 5 × 106) in solution has been determined by the transient electric birefringence method. The analysis of the birefringence decay makes it possible to study only the higher-molecular-weight fraction, the molecules being considered as rigid elongated particles in a short time scale. A marked concentration dependence of the relaxation time has been observed for DNA in low ionic strengths. Above a critical concentration c*, τ3 increases with the DNA concentration, c. The value of c* increases with the ionic strength. For 10-3 ionic strength (with NaCl), c* is about 10 μg/mL; then we observe the same strong concentration dependence of rotational relaxation times as recently reported for rodlike M-13 viruses [Maguire, J. F., McTague, J. P. & Rondelez, F. (1980) Phys. Rev. Lett. 45, 1891-1894]. These results may be discussed in terms of the Doi-Edwards theory for rotational relaxation time of rigid macromolecules [Doi, M. (1975) J. Phys. 36, 607-611; Doi, M. & Edwards, S. F. (1978) J. Chem. Soc. Faraday Trans. 74, 918-932] and the critical concentration above which the interactions between the molecules begin to appear allows determining the corresponding molecular length. We observe a very good agreement between the DNA lengths obtained from the c* values and by using the infinite dilution value of τ3 and Broersma's equation. Therefore, only highly diluted solutions can be used if intrinsic molecular properties based on the rotational diffusion of high-molecular-weight elongated molecules are studied.
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    Biopolymers 22 (1983), S. 2411-2421 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A thermodynamic treatment of the helix-coil transition of synthetic polypeptides in binary organic solvent mixtures is extended to describe isobaric heat-capacity increments associated with the phenomenon. This development resolves such increments into three components: two associated respectively with intrinsic differences between the ordered and disordered states of the macromolecule and between the coil-solvent complex and its components, and a third term derived from the temperature dependence in the fraction of coil residues bound to active solvent. Insights derived from this analysis are also applied to the discussion of some heat capacity increments associated with the denaturation of globular proteins.
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 22 (1983), S. 2507-2511 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 22 (1983), S. 2539-2547 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The temperature dependence of the humidity-sensitive spacing, d, related to the lateral packing of collagen molecules was measured for fully hydrated collagen. In the vicinity of 0°C, a sudden change in d was observed, which was reversible with temperature. In the diffraction profile, below 0°C, a set of diffraction peaks identified with the hexagonal crystalline form of ice was observed. With the reduction in water content, the intensity of the set of diffraction peaks decreased and was found to be zero at a water content of 0.38 g/g collagen. These results were considered to be caused by the frozen water in collagen fibril below 0°C. According to the water content dependence of d, it was considered that up to a certain water content water absorbed would be stowed in the intermolecular space of collagen and above that water content water molecules would aggregate to make pools, i. e., extrafibrillar spaces. The unfreezable bound water was considered to be located in the intermolecular space of collagen. Size of the extrafibrillar space, determined from the intensity analysis of a smallangle x-ray scattering pattern, corroborates the speculation that the water showed in the extrafibrillar space is freezable and free. The formation of the hexagonal crystalline form of ice in the extrafibrillar space was considered to cause the sudden change in d at 0°C.
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    Chemie in unserer Zeit 14 (1980), S. 72-72 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 14 (1980), S. 73-81 
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    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 14 (1980), S. 124-133 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 14 (1980), S. 176-176 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 14 (1980), S. 168-175 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 14 (1980), S. 197-207 
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    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 14 (1980), S. 209-209 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 17 (1983), S. 67-67 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 17 (1983), S. 67-67 
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    Chemie in unserer Zeit 17 (1983), S. 77-84 
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    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 17 (1983) 
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    Chemie in unserer Zeit 17 (1983), S. 202-202 
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    Keywords: Chemistry ; Chemistry
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