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  • 1984  (10,328)
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  • 101
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    New York : Wiley-Blackwell
    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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  • 102
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    Biopolymers 22 (1983), S. 2169-2172 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 103
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    Biopolymers 22 (1983), S. 2207-2217 
    ISSN: 0006-3525
    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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  • 104
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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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  • 105
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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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  • 106
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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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  • 107
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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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  • 108
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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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  • 109
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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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  • 110
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    Biopolymers 23 (1984), S. 1917-1930 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solution-phase Raman spectra of diastereomeric alanyl dipeptides, D-Ala-L-Ala and L-Ala-L-Ala, and various mono- and dideuterated isotopomers in H2O and D2O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupled-oscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.
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  • 111
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    Biopolymers 23 (1984), S. 1951-1960 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational equilibria of five β-cellobiose conformers have been studied theoretically in 10 solvents. The stability of the conformers in dilute solution has been compared by using the method that has already been tested for 2-methoxytetrahydropyran, β-maltose, and D-glucose. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from the properties of the solute calculated by the PCILO quantum-chemical method and physicochemical properties of the solvents. The calculated abundance of conformers depends on the solvent (e.g., in dioxane C1:C2:C3:C4:C5 = 60.0:34.1:2.9:2.0:1.0; in dimethylsulfoxide, 75.5:22.1:1.8:0.5:0.2; and in water, 82.2:16.2:1.3:0.2:0.1). The results obtained indicate that the preponderant conformer in the aqueous solution is similar to the one adopted by β-cellobiose in the crystalline form. The role of individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and nmr parameters have been calculated and compared with observable properties. The marked differences observed between solvent-induced conformational changes for β-cellobiose and β-maltose have been discussed from the viewpoint of the solubility of the cellulose.
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  • 112
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg+, Glu-, and Asp-) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys+, Arg+, and His+) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G-X 〉 C-X 〉 A-X U-X or T-X, and G · C-X 〉 A · T(U)-X, where X is one of these amino acid residues. It has been shown that Glu- and Asp- can recognize guanine in single-stranded nucleic acids; Arg+ can recognize G · C base pairs from A · T base pairs in double-stranded structures.
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  • 113
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 114
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    Biopolymers 23 (1984), S. 2195-2210 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of histone H1 on the conformation and stability of control and acetylated HeLa high-molecular-weight chromatin that had been stripped of H1 and nonhistone proteins was compared by circular dichroism (CD) and thermal denaturation measurements. Two different preparations of H1, originating from rat thymus and chicken erythrocyte, were used in the reconstitution studies. The control and acetylated stripped chromatin had identical CD and thermal denaturation properties, as did their reconstitutes with rat thymus H1. Reconstitutes of the two chromatins with chicken erythrocyte H1 had similar CD properties, but thermal denaturation studies showed that the acetylated reconstitute was destabilized compared to the control reconstitute. Reconstitutes of both chromatins with chicken erythrocyte H1 had a more condensed and stabilized structure than the reconstitutes with rat thymus H1. Thus, acetylation caused a decrease in the stability of chromatin in the presence of erythrocyte H1, but more marked differences were detected in the structure of stripped chromatin after reassociation with different H1 preparations.
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  • 115
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Human fibrinogen was treated with thrombin in the presence of fibrinoligase (Factor XIIIa) and calcium ion at pH 8.5, ionic strength 0.45, and the ensuing polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of γ-γ ligation was determined from the former. The latter provided the size distribution of ligated end-to-end sequences produced by splitting the ligated staggered overlapped oligomers down the middle, for degrees of polymerization, x, from 1 to 10. Addition of fibrinoligase (in which the activating thrombin had been inhibited by p-nitrophenyl-p′-guanidinobenzoate, NPGB) to Kabi fibrinogen showed the presence of small amounts of ligatable oligomers. Addition of fibrinoligase to a polymerizing mixture in which the action of thrombin had been stopped before clotting by NPGB produced the same distribution of ligated end-to-end sequences that was obtained when fibrinoligase was originally present, at least for reaction times up to 0.7 of the clotting time. The kinetics of γ-γ ligation by fibrinoligase acting on a polymerized mixture stabilized by NPGB were followed. The reaction was first order in the concentration of ligatable γ-γ junctions and the initial velocity was proportional to the enzyme concentration. The time evolution of size distribution of ligated end-to-end sequences agreed with a theory based on random ligation of ligatable junctions.
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  • 116
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    Biopolymers 23 (1984), S. 201-212 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A mean-square helical hydrophobic moment, 〈h2〉, is defined for polypeptides in analogy to the mean-square dipole moment, 〈μ2〉, for polymer chains. For a freely jointed polymer chain, 〈μ2〉 is given by Σmi2, where mi denotes the dipole moment associated with bond i. In the absence of any correlations in the hydrophobic moments of individual amino acid residues in the helix, 〈h2〉 is specified by ΣHi2, where Hi denotes the hydrophobicity of residue i. The tendency for correlations in orientations of residue hydrophobic moments in helices therefore dictates the size of 〈h2〉/〈H2〉, where 〈H2〉 denotes the average value of ΣHi2 for all helices. The value of 〈h2〉/〈H2〉 will be greater than one in amphiphilic helices. A necessary prerequisite for this diagnostic usage of 〈h2〉/〈H2〉 is that the residue hydrophobic moment be oriented prependicular to the principal axis of the helix. Matrix-generation schemes are formulated that permit rapid evaluation of 〈h2〉 and 〈H2〉. The behavior of 〈h2〉/〈H2〉 is illustrated by calculations performed for model sequential copolypeptides.
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  • 117
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    Biopolymers 23 (1984), S. 271-285 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report a calculation of the distribution of small ions around a charged cylinder representing a polyelectrolyte molecule in solution. The Monte Carlo method of Metropolis, Rosenbluth, and Teller was used to avoid the inaccuracies known to be associated with the Poisson-Boltzmann equation. The systems examined contained a long polyelectrolyte cylinder with charge parameter, χ, equal to 4.2, corresponding approximately to a DNA molecule. In one model, the cylinder had charges on its axis and an exclusion radius to the center of the small ions equal to 10 Å, while the small ions had various radii in the range from 1 to 10 Å and one or two protonic charges. Various systems were studied; some had one species of small ion alone, others had mixtures of different types. The results showed good agreement with the solution of the Poisson-Boltzmann equation when only the species with 1-Å radius was present, but considerable discrepancies appeared with larger ions as a result of excluded volume interactions between the latter. Deviations from the Poisson-Boltzmann equation also appeared when both positive and negative small ions were present; the deviations were in the direction of a higher concentration of both counter- and co-ions, but particularly co-ions, close to the polyelectrolyte. In another model, the charges were arranged along two helices on the surface of the cylinder; the resulting radial distribution of small ions was not much different from that found when the charges were situated on the axis. In all cases there was a striking accumulation of counterions in a layer of concentration exceeding 1 mol/L at the surface of the polyion.
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  • 118
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    Biopolymers 23 (1984), S. 337-351 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Brillouin scattering was used to determine the longitudinal acoustic velocity along the axis of collagen fibers as the relative humidity decreased from 95 to 0%. Between 0 and 86%, the velocity decreased linearly at a modest rate. Above 86%, the decrease was steep. The changing mass of the absorbed water accounts for most of the velocity change in the lower humidity range. The remaining deviation is probably due to variation of the elastic coupling between molecules. At low humidity, the adsorbed water is known to be attached to the collagen molecules, whereas the additionally adsorbed water at high humidity has the properties of bulk liquid. The high-humidity sonic velocity variation is ascribed to the presence of free water. It is possible to identify the five water regimes of Pineri et al. [(1978) Biopolymers 17, 2799-2815] with the variations of the sonic velocity with water content.
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  • 119
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    Biopolymers 23 (1984), S. 353-361 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Optical rotation, viscosity, and density studies are reported on solutions of α-gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.
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  • 120
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 121
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have recorded high-resolution 13C-nmr spectra of collagen fibrils in the solid state by the cross-polarization-magic-angle-spinning(CP-MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference 13C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 31-helical polypeptides [(Gly)nII, (Pro)nII, (Hyp)n, and (Ala—Gly—Gly)nII], and the triple-helical polypeptides [(Pro—Gly—Pro)n and (Pro—Ala—Gly)n]. Examination of the 13C chemical shifts of these polypeptides, together with our previous data, showed that the 13C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the 13C chemical shifts of Ala residues of the 31-helical (Ala—Gly—Gly)n and triple-helical (Pro—Ala—Gly)n are significantly displaced, compared with those of the α-helix, β-sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen-like polypeptides. Further, the 13C chemical shifts of Gly and Pro residues in the triple-helical polypeptides are substantially displaced from those found in (Gly)nII and (Pro)nII of the 31-helix, reflecting further conformational change from the 31-helix to the supercoiled triple helix. In particular, the 13C chemical shifts of Gly C = O carbons of the triple-helical polypeptides are substantially displaced upfield (4.1-5.1 ppm), with respect to those of the 31-helical polypeptides. These displacements are interpreted by that Gly C = O of the former is not involved in NH … O = C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds.On the basis of these 13C chemical shifts, as reference data for the collagenlike structure, we were able to assign the 13C-nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.
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  • 122
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    Biopolymers 23 (1984), S. 2349-2360 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dermorphin (Tyr—D-Ala—Phe—Gly—Tyr—Pro—Ser—NH2), a potent natural peptide opioid, its synthetic L-Ala2 analog, and all the N fragments from the tripeptide (Tyr—D-Ala—Phe—NH2) to the parent hexapeptide amide were characterized for the first time by means of proton nmr spectroscopy at 11.74 T. Assignments of most protons of dermorphin were facilitated by the study of the N-terminal fragments. Comparison of spectroscopic parameters with relative pharmacological activity is proposed as a possible means of studying flexible agonists in solution.
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  • 123
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    Biopolymers 23 (1984), S. 2715-2724 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′-diphosphate reveals that, for each species, the uv-absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA and RNA.
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  • 124
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    Biopolymers 23 (1984), S. 2963-2966 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 125
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    Biopolymers 23 (1984), S. 719-734 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aggregation of poly(γ-benzyl-α,L-glutamate) and its enantiomer in toluene has been investigated by following the viscosity as a function of temperature, concentration, molecular weight, molecular-weight distribution, helix chirality, and shear rate. The temperature and concentration data for a 138,000-molecular-weight sample was fitted to an open, reversible end-to-end aggregation model. The aggregation numbers resulting from this fit were consistent with the sudden onset in non-Newtonian flow resulting from only a 0.2-wt% increase in concentration. The association equilibrium constant was then used to predict viscosity for comparison with other data, in particular, the effect of molecular weight and molecular-weight distribution. A mixture of right-and left-handed helices showed the aggregation was not chiral selective. The stiffness of end-to-end aggregated (hydrogen-bonded) molecules differed little from their covalent counterparts, at least below a molecular weight of ∼106. We conclude that polybenzylglutamate aggregation in toluene can be described by an open end-to-end aggregation model.
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    Biopolymers 23 (1984), S. 797-808 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quasielastic light-scattering (QELS) studies were performed on a monodisperse preparation of dinucleosomal-sized DNA having an average of 375 base pairs. The QELS data were obtained at several time intervals at each angle examined over the range 30° 〈 θ 〈 60° for the ionic strength solvents 500, 50, 10, and 1 mM in KCl. What results from this study is that two relaxation domains persist over the entire ionic strength range where the “splitting” between these two domains increases as the ionic strength is lowered. The ordinate intercept of Dapp vs Cp/2Cs, where Cp is the polyion concentration and Cs is the added salt concentration, is shown to give the “true” hydrodynamic value for the diffusion coefficient. The “splitting phenomenon” is interpreted in terms of two models currently in vogue: small ion-polyion coupled modes and translational-rotational coupled modes for rigid rods in congested solutions. Although neither model is in perfect agreement with the experimental results, the small ion-polyion coupled mode theory appears to provide a better quantitative description of the observations.
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    Biopolymers 23 (1984) 
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    Chemie in unserer Zeit 15 (1981), S. A4 
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    Notes: Using classical potential functions, we carried out potential-energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum-energy conformations of the complexes are close to DNA A- and B-family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low-energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are discussed.
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    Notes: To exemplify the usefulness of the S-tert-butylthio group for a reversible blocking of the cysteine thiol function in peptide synthesis, fully protected dihydrosomatostatin was prepared by the fragment-condensation procedure. The experimental results confirm the excellent stability of the asymmetric disulfide under the normal conditions of peptide synthesis and prove that the selective, acid-catalyzed nucleophil removal - as well as by mercaptans - of the 2-nitrophenylsulfenyl group proceeds smoothly in the presence of this thiol protection. Thus, the strategy of overall acid-labile side-chain protection in combination with the Nα-2-nitrophenylsulfenyl group for the chain-elongation steps can be successfully applied to the synthesis of cysteine-containing peptides using their S-tert-butylthio derivatives. Removal of the acid-labile groups, followed by reductive cleavage of the asymmetric disulfides and successive air oxidation, allowed a clean conversion of protected dihydrosomatostatin into somatostatin at a high degree of purity and in good yields.
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    Biopolymers 20 (1981), S. 129-139 
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    Topics: Chemistry and Pharmacology
    Notes: The translational friction coefficients, rotational friction coefficient, and intrinsic viscosity of rigid regular structures composed of up to eight identical spherical subunits have been accurately calculated. The aim of this calculation is to interpret the hydrodynamic properties of oligomeric subunit proteins. To avoid the well-known failure of the theory in the evaluation of rotational coefficients and intrinsic viscosities, each subunit is hydrodynamically modeled as a polyhedral array of smaller spheres. The analysis of several alternatives suggests that a cubic array is the best choice. The reliability of this strategy is checked by comparison of the calculated values for all the transport properties of a sphere and the translational friction coefficients of a dimer with their exact values. Finally, the hydrodynamic properties of a number of subunit structures with varying number of subunits and different geometries are tabulated.
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    Biopolymers 20 (1981), S. 89-109 
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    Topics: Chemistry and Pharmacology
    Notes: The conformation and dynamic structure of single-stranded poly(inosinic acid), poly(I), in aqueous solution at neutral pH have been investigated by nmr of four nuclei at different frequencies: 1H (90 and 250 MHz), 2H (13.8 MHz), 13C (75.4 MHz), and 31P (36.4 and 111.6 MHz). Measurements of the proton-proton coupling constants and of the 1H and 13C chemical shifts versus temperature show that the ribose is flexible and that base-base stacking is not very significant for concentrations varying from 0.04 to 0.10M in the monomer unit. On the other hand, the proton T1 ratios between the sugar protons, T1 (H1′)/T1 (H3′), indicate a predominance of the anti orientation of the base around the glycosidic bond. The local motions of the ribose and the base were studied at different temperatures by measurements of nuclear Overhauser enhancement (NOE) of protonated carbons, the ratio of the proton relaxation times measured at two frequencies (90 and 250 MHz), and the deuterium quadrupolar transverse relaxation time T2. For a given temperature between 22 and 62°C, the 13C-{1H} NOE value is practically the same for seven protonated carbons (C2, C8, C1′, C2′, C3′, C4′, C5′). This is also true for the T1 ratio of the corresponding protons. Thus, the motion of the ribose-base unit can be considered as isotropic and characterized by a single correlation time, τc, for all protons and carbons. The τc values determined from either the 13C-{1H} NOE or proton T1 ratios, T1(90 MHz)/T1(250 MHz), and/or deuterium transverse relaxation time T2 agree well. The molecular motion of the sugar-phosphate backbone (O-P-O) and the chemical-shift anisotropy (CSA) were deduced from T1 (31P) and 31P-{1H} NOE measurements at two frequencies. The CSA contribution to the phosphorus relaxation is about 12% at 36.4 MHz and 72% at 111.6 MHz, corresponding to a value of 118 ppm for the CSA (σ = σ∥ - σ⊥). Activation energies of 2-6 kcal/mol for the motion of the ribose-base unit and the sugarphosphate backbone were evaluated from the proton and phosphorus relaxation data.
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    Notes: Kinetic studies of spin interconversion in various derivatives of metmyoglobin such as the fluoride, aquo, hydroxide, azide, imidazole, and cyanide were performed by the coaxial-cable temperature-jump method. For all these derivatives, except fluoride and aquomyoglobin, a single relaxation was observed around 3 μsec. The rate constants and activation parameters for the spin interconversion were estimated and are discussed in comparison with those reported for the reaction of synthetic iron complex. Other hemoproteins such as cytochrome c and human hemoglobin were also examined, and the results were compared with those for myoglobin. The effect of buffer solution is also discussed.
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    Biopolymers 20 (1981), S. 201-207 
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    Topics: Chemistry and Pharmacology
    Notes: Transient electric dichroism has been measured for a Cu(II)-bovine serum albumin (BSA)-2-(2-pyridylazo)-1-naphthol (αPAN) complex at pH 5.5-12. From the magnitude of the reduced linear dichroism and the disorientation rate of the oriented chromophore, at least three kinds of binding states of Cu(αPAN)+ complex exist. They are present predominantly at pH 5.5-10, 7.5-10, and 10-12, with the αPAN plane approximately parallel, vertical, and parallel with respect to the oriented axis of a BSA molecule.
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    Biopolymers 20 (1981), S. 241-242 
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  • 166
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    Topics: Chemistry and Pharmacology
    Notes: Dynamic light-scattering techniques are employed to study the internal Brownian motions of a commercial calf thymus DNA, clean and contaminated φ29 DNAs, and a clean φ29 DNA with bound spermidine as a function of pH. The Rouse-Zimm model parameters of both calf thymus and contaminated φ29 DNAs differ substantially from those of clean φ29 DNA in the neutral-pH region. However, this difference is largely removed by adding 0.01M EDTA (which has no effect on clean φ29 DNA) to the calf thymus DNA sample. These findings imply the existence in that preparation of polycation contaminants, presumably basic proteins, that can substantially alter the local mechanical properties of the DNA near their binding sites. The internal motion parameters kBT/f and b of both calf thymus and contaminated φ29 DNAs are found to exhibit pronounced characteristic variations between pH 8.5 and 10.5, over which range there is essentially no detectable titration to a resolution of about 1% of the base pairs. These variations, which are not observed for clean φ29 DNA, are qualitatively similar to those previously reported for a φ29 DNA with 21 single-strand breaks per chain. This indicates the formation of titratable joints associated with bound polycation contaminants. These basic ligands presumably facilitate local denaturation by stabilizing the titration of one or more protons on base-ring nitrogens near their binding sites. Spermidine binding up to 85-87% of neutralization of the total DNA charge has only a relatively minor effect on the internal motion parameters at neutral pH in 0.01M NaCl. However on raising the pH to 10.2, the internal motion parameter kBT/f undergoes a marked decrease similar to that observed for both calf thymus and contaminated φ29 DNAs and also φ29 DNA with single-strand breaks. This indicates that spermidine, too, is capable of inducing titratable joints. Evidence is presented that the titratable joints associated with bound polycations on the calf thymus DNA may serve primarily as torsion joints, as was found previously for the titratable joints associated with single-strand breaks.
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    Biopolymers 20 (1981), S. 787-801 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Receptors are functional membrane proteins on the cell surface that recognize external signals and trigger biological responses by generating intracellular signals. Due to prolonged exposure to external signals, receptors are often desensitized and no longer produce intracellular signals. This simple control mechanism may work without negative-feedback regulation from another molecule if the active state of a receptor reflects a transient metastable molecular structure. A theoretical framework is developed to identify a metastable state associated with a conformational transition of protein molecules, in which a transient state can be observed somewhat above the equilibrium transition point. The conducting state of the acetylcholine receptor may thus represent a metastable state associated with a conformational transition from the resting state to the desensitized state. Similarly, the conducting state of the voltage-sensitive sodium channel may represent a metastable state associated with a conformational transition from the resting state to the refractory state. The rates of appearance and disappearance of the transient state, as well as the equilibrium ratio of the two preexisting states, can be estimated from the free energy of protein structure. The appearance of the transient state is generally a multirelaxation process and may show a time lag, while the disappearance is a slower single-relaxation process.
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    Biopolymers 20 (1981), S. 853-864 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: We have estimated the absorption of microwave radiation by the four acoustic modes of poly(dG)·poly(dC) in B conformation. The eigenvectors used in this calculation are those obtained from a refined normal coordinate analysis by fitting the velocity of the longitudinal acoustic mode to that observed by Brillouin scattering. The acoustic modes couple to the radiation field when translational invariance is broken such as for finite segments of helix and as may be the case in vivo. Calculations for various helix lengths show that the estimated absorption is greater than that of water by at least two to three orders of magnitude in some cases.
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    Biopolymers 20 (1981), S. 901-913 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The biologically active ACTH(1-32) and ACTH(1-24) and other shorter peptide segments of the native hormone ACTH(1-39) were studied in aqueous solution by 13C-nmr. In order to identify the 13C resonances - except those of the carbonyls - both high-field nmr spectroscopy measurements and substitution of residues with amino acids enriched to 85% in 13C were carried out. The main results are (1) the direct characterization of the cis-trans isomerism of proline 24 and its effects on the directly connected and sequentially neighboring residues and (2) findings that the conformational features agree with an α-helix type organization in the N-terminal part of the ACTH molecule which is responsible for the biological activity.
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    Topics: Chemistry and Pharmacology
    Notes: This article reports on both (1) the precision and capability of a computerized multidimensional spectrophotometric system recently developed in our laboratory and (2) the high-resolution study of the helix-coil transition of poly(L-glutamic acid)[poly(Glu)], especially with regard to the discovery of an overlooked transition which is attributable to order-disorder rearrangement of the poly(Glu) side chain in the α-helical conformation. This study was made possible by the high performance of the system used. The simultaneous and continuous measurement of the circular dichroism, the absorbance and light-scattering intensity, and the pH titration curve of poly(Glu) in aqueous salt solution was carried out under continuous scanning of pH ranging from 8 to 2. Besides the well-known random coil to α-helix transition that occurs at about pH 5.5, a highly cooperative transition, which is indicated as a small but definite step in several spectral dimensions, is observed for the first time at pH 4.3. The transition is ascribed to an order-disorder conversion of the side chain on the α-helix backbone.
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    Notes: The interaction of tilorone with DNA and five synthetic polydeoxyribonucleotides [(I): poly[d(A-T)]·poly[d(A-T)]; (II): poly[d(A-C)]·poly[d(G-T)]; (III): poly[d(G-C)]·poly[d(G-C)]; (IV): poly(dG)·poly(dC); and (V): poly(dA)·poly(dT)] has been investigated. Binding isotherms for the homopolymers were obtained by microdialysis equilibria using 14C-labeled tilorone and interpreted with different models: exclusion effect, associated or not associated with cooperativity, or variable exclusion. Affinity appears to be related more to local structure than to base composition and decreases in the following order: (I) 〉 (II) 〉 (III) 〉 (IV) 〉 (V). Intercalation in circular DNA was demonstrated by electrophoresis migration and electron microscopy, which yielded an average unwinding angle of 7° per bound dye. The behavior observed in CD and UV spectroscopy shows a sequence similar to the affinities. Tilorone seems to be less intercalated in (IV) and not at all in (V). The experimental binding isotherm of tilorone to DNA was well fitted on the basis of a model where DNA acts as a heterogeneous lattice built with the six different possible couples of adjacent base pairs, each potential site behaving as if it were in the corresponding homopolymer. The results are discussed in terms of specificity of alternating Pyr-Pur sequences and related to theoretical calculations on intercalation energies of DNA.
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  • 172
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    Biopolymers 20 (1981), S. 817-831 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Isopiestic vapor pressure measurements of the ternary systems water + triglycine + urea and water + glycine-L-alanine + urea were made and used to calculate the Gibbs free energy of these systems. Together with recently published analogous results on systems, in which the first solute was glycine or alanine or diglycine, and measurements of the excess enthalpy of all these solutions, it is possible to calculate the Gibbs free energy of transfer and the enthalpy of transfer of the peptide group from water to aqueous urea solutions. The transfer can be described as a binding of urea to the peptide group with ΔG = -1.85 kJ mol-1 and ΔH = -18.7 kJ mol-1 at 298.1 K.
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  • 173
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    Biopolymers 20 (1981), S. 891-899 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complex formation of valinomycin with Ba2+ ions was investigated by circular dichroism spectroscopy. The results indicated that Ba2+ forms entirely different types of complexes when compared with K+. The data with perchlorate salt showed evidence for the formation of less stable V2C (peptide sandwich), VC (1:1), and VC2 (ion sandwich) complexes followed by a stable final complex upon gradual addition of salt (V stands for valinomycin and C for the cation). This final complex possibly has a flat structure with no internal hydrogen bonds, similar to that of valinomycin in highly polar solvents. The possible complexation mechanism and the role played by anions and isopropyl side chains are highlighted.
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  • 174
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    Biopolymers 20 (1981), S. 967-975 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The unwinding of DNA strands in the presence of small concentrations of Mn2+ ions (2 × 10-4-4 × 10-4M) has been studied. The process of unwinding is nonequilibrium; the DNA strands are gradually unwound at a constant temperature corresponding to the beginning of the melting curve. There is no true renaturation in the partially melted DNA. It is shown in the paper that these effects are due to the aggregation of the unwound DNA regions. The Mn2+ ions are responsible for the binding of the unwound strands. The aggregation precludes renaturation, shifts the equilibrium towards the melted state, and causes slow unwinding at a constant temperature. The binding of denaturated regions seems to occur through the guanines.
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  • 175
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    Topics: Chemistry and Pharmacology
    Notes: Combined three- and four-terminal AC bridge measurements have been made at frequencies from 10 Hz to 100 KHz on samples of DNA with different molecular weight in aqueous solution under varying conditions of DNA concentrations and added salt. A method is described for the separation of large quantities of DNA fractionated according to size. A complicated pattern of dependence of the specific dielectric increment on concentration is found, and the difficulties of comparing the results from sample to sample are discussed. The dielectric properties of the fractionated samples of DNA in aqueous solution are reported for solutions sufficiently dilute that specific dielectric increment is independent of concentration. The specific dielectric increment of the solutions (with concentration measured in moles of DNA molecules/liter) is found to increase as the square of the molecular weight. The results are compared with results of polyelectrolyte theories which deal explicitly with counterion fluctuations and interactions. The frequency dependence of the dispersion is much broader than for simple Debye relaxation. It is satisfactorily fitted by the empirical Cole-Cole circular are function and the breadth of the dispersion is found to be, if anything, less for the fractionated samples than for native DNA in solution.
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  • 176
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 177
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    Biopolymers 20 (1981), S. 1113-1122 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The gel filtration method was applied to the study of the interaction of the metachromatic cationic dye methylene blue (MB) with heparin in aqueous solution. This method requires the determination of the total MB concentration in the effluent. It was found that (i) MB in aqueous solution can be extracted quantitatively with benzyl alcohol (BzlOH), (ii) the metachromatic effect of MB is not observed in BzlOH, and (iii) the presence of heparin in aqueous solution does not interfere in the BzlOH extraction of MB. Accurate determination of MB concentration in the effluent can be made by extraction of MB with BzlOH, followed by the usual absorption spectroscopy. In addition, the use of the spectrophotometric method with this procedure entailed no serious problem relating to adsorption of MB on the glass walls. Gel filtration binding experiments were successfully carried out on a Sephadex LH-20 column using 0.005M acetate buffer as effluent. The binding data obtained were analyzed in terms of the cooperativity parameter according to the method of Schwarz. The thermodynamic parameters for the binding process of MB were also evaluated. It is shown that the binding of MB to heparin is highly cooperative, exothermic, and stabilized by entropic factors.
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  • 178
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    Biopolymers 20 (1981), S. 1147-1159 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quasielastic and static light-scattering measurements were made on DNA isolated from chicken erythrocyte mononucleosomes as a function of ionic strength between 6 × 10-4 and 1.0M. A transition from single-exponential autocorrelation functions to markedly non-single-exponential decays was observed around 10-2M ionic strength and was accompanied by a large decrease in the excess light-scattering intensity. Autocorrelation functions recorded below 10-2M salt were well fit by the sum of two exponential relaxation which differed by as much as 100-fold in time constants. Apparent diffusion coefficients for the fast and slow processes plateaued around 10-3M with numerical values approximately 10-fold and 1/10, respectively, of the translational diffusion coefficient for mononucleosome DNA at high ionic strength. This behavior is similar to that observed with poly(L-lysine), for which the slow decay has been associated with a transition to an extraordinary phase. The strong and complex salt dependence observed here illustrates potential difficulties in deriving structural information from scattering by polyions at low ionic strength.
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  • 179
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    Biopolymers 20 (1981), S. 1261-1270 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A variety of solution conditions are known to induce collapse of linear DNA into a compact configuration without dramatic change of local structure. When visualized, these compact forms frequently have a toroidal appearance. We ask whether the molecular basis of the toroidal shape can be a stable curvature of isolated rodlike DNA segments. Application of the classical Euler-Lagrange theory for the buckling of elastic rods provides us with an affirmative answer. Specifically, we see that, in principle, sufficient addition of inert polymer to DNA solutions can induce buckling of DNA segments. However, no attempt is made to quantitate the Euler-Lagrange condition for sufficiency in terms of added polymer concentration. We find also that complete neutralization of the phosphate charge is more than sufficient to induce buckling of DNA segments of length comparable to a Kuhn segment. The quantitative argument involves comparison of buckling forces provided by polyelectrolyte theory with the Euler-Lagrange criterion. Knowledge of the ionic-strength dependence of DNA bending stiffness (persistence length) is not required.
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    Biopolymers 20 (1981), S. 621-624 
    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 20 (1981) 
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  • 182
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    Biopolymers 20 (1981), S. 629-632 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 183
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    Topics: Chemistry and Pharmacology
    Notes: The protein actinoxanthin (molecular weight 10,300) crystallizes in space group P212121, with cell dimensions a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and z = 4. The three-dimensional structure of actinoxanthin at 4-Å resolution was determined by x-ray methods on the basis of experimental data from the native protein and five isomorphous derivatives. At the stage of solving the phase problem, the heavy atoms in the derivatives were located using direct methods. The actinoxanthin molecule can be described as an oblate ellipsoid with approximate dimensions 20 × 30 × 40 Å and consists of two different sizes of folded units separated by a well-defined cleft. The larger unit, including the N- and C-terminals of the protein chain, is characterized by a significant content of β-sheet structure. The smaller unit, containing two deca- and hexapeptide cycles closed by disulfide bonds, has a mainly irregular structure.
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    Biopolymers 20 (1981), S. 753-763 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo method is presented to calculate equilibria for the binding of ligands to one-dimensional heteropolymers. Equivalency with other methods suitable for particular cases was verified (i.e., matrix and combinatorial methods). The principal interest of this Monte Carlo method is in its facility for adaptation to any physically conceivable binding model and that it gives access to the parameters accounting for partial binding to each different type of site. General properties of binding isotherms with excluded-site effects and relations between partial binding ratios and partial free site ratios are discussed. An effective calculation is presented for illustration of the method.
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  • 185
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    Biopolymers 20 (1981), S. 1565-1573 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The vacuum-ultraviolet circular dichroism (VUCD) of chondroitin and chontroitin-6-sulfate has been measured to 160 nm for films and to 170 nm for D2O solutions. The pD-dependent dichroic behavior of these glycosaminoglycans in D2O is similar above 200 nm and is in agreement with previous studies. Near 190 nm, the CD band sign is also dependent on pD. VUCD spectra were recorded for films and solutions of poly(L-arginine). In trifluoroethanol the polypeptide is α-helical, while in D2O it exists as a random coil. The well-characterized coil-helix transition of poly(L-arginine) during complexation with chondroitin-6-sulfate was observed by VUCD, including the previously inaccessible entire π → π* band. By construction of difference spectra it was also possible to monitor the VUCD of the polysaccharide component during complexation.
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  • 186
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    Biopolymers 20 (1981), S. 1589-1603 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Investigations of DNA using CD spectroscopy show that the P-form is available in a wide variety of methanol-ethanol mixtures when the water content is low. Increasing the temperature or the ethanol content of a 95% methanol solution causes DNA to undergo a cooperative transition to the P-form. However, this transition cannot be reversed on cooling, or on adding methanol. Thus P-form DNA appears to be stable at high methanol concentrations, but it is usually not observed because the DNA is trapped by a kinetic barrier. P-form DNA will instantaneously assume the native B-form on addition of water, confirming earlier reports that P-form DNA is not strand separated [E. Kay (1976) Biochemistry 15, 5241]. CD spectra extended to 190 nm show that there is no base-base interaction in the P-form. However, the P-form is extremely stable to heat denaturation in solvents which promote hydrogen bonding between the base pairs. A number of models that can account for the properties of P-form DNA are discussed.
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  • 187
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    Biopolymers 20 (1981), S. 1651-1669 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Approximate methods are developed and evaluated for treating the rate of binding ligands that cover several contiguous sites to a homogeneous one-dimensional lattice, which represents a nucleic acid or other linear biopolymer. The model requires as input only the number of lattice sites necessary for binding, the total number (possibly infinite) of lattice sites, and elementary rate constants for the cooperative and noncooperative association and dissociation of the ligand on the lattice. The computational methods employed are an extension of the triplet closure approximation from the helix-coil (single-site ligand) problem to the large ligand binding problem. It is found that consideration of clusters of n + 2 lattice sites, where each ligand covers n sites, gives a surprisingly accurate description of the kinetics. The approximation is implemented by an extension of the matrix-iteration approach proposed by Craig and Crothers. The effects of the finite lattice length, as well as the capability to treat ligand motion along the lattice, are incorporated. When all symmetries are taken into consideration, the time required for the matrix iteration calculation rises only linearly with the ligand length n and is considerably less than that of the Monte Carlo method, which is used as a standard for comparison.
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  • 188
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    Topics: Chemistry and Pharmacology
    Notes: Improved chemical synthesis of bovine pancreatic ribonuclease (RNase) A was achieved by applying a new deprotecting procedure with trifluoromethanesulfonic acid-thioanisole in combination with a modified air-oxidation procedure with glutathione for the disulfide formation. After purifications by affinity chromatography, followed by ion-exchange chromatography, a protein with the full enzymatic activity was obtained and subsequently crystallized from aqueous ethanol according to Kunitz. A totally synthetic enzyme with full RNase A activity was thus obtained in a crystalline form for the first time.
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  • 189
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    Biopolymers 20 (1981), S. 1901-1912 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: After a brief review of the genesis of cyclic peptide research, some current areas of interest in this field are examined. The final section of this manuscript considers some possible future directions of research with cyclic peptides.
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  • 190
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    Biopolymers 20 (1981), S. 1949-1958 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Important aspects in detailed nmr analyses of the conformations of linear peptides are discussed using enkephalin and the α-mating factor of Saccharomyces cerevisiae as examples. The cationic, dipolar, and anionic forms in dimethyl sulfoxide solution may be identified by ir analyses. Because of the electrostatic interaction between the N- and C-terminal groups, the dipolar form of enkephalin takes the folded conformation, as well as extended conformation(s), in dimethyl sulfoxide solution. Such conformational equilibrium is responsible for anomalous temperature dependences and solvent-composition dependences of the amide and Cα proton chemical shifts. Active analogs, enkephalinamide and enkephalinol, take extended conformation(s) in solution. These opioid peptides probably take a specific active conformation upon binding with a receptor. For the α-mating factor and active peptide analogs in aqueous solution, a folded conformation with two βturn structures is responsible for the biological activity.
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  • 191
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    Biopolymers 20 (1981), S. 1989-1999 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The comparative study of proteins which differ in primary structure by point mutations permits one to use thermodynamic experiments to obtain information about the role of specific amino acids in determining protein structure and stability. We have now determined the thermodynamic changes induced in six mutants of T4 lysozyme and have compared the results with the wildtype enzyme. Our work is in collaboration with B. Matthews and his colleagues, who have determined the crystal structure of T4 lysozyme and have obtained difference Fourier maps for four of the mutants. The ultimate aim is to correlate changes in protein stability with changes in the detailed structure of the protein. This paper discusses the thermodynamic results obtained from the mutants studied. All the mutants have a lower Tm than the wild-type enzyme and changes in the enthalpy of denaturation are sometimes extraordinarily large. Changes in ΔH of denaturation are usually accompanied by compensating changes in ΔS. The general question of protein stability and the manner in which it varies with temperature and mutations is discussed.
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    Biopolymers 20 (1981) 
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  • 193
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    Topics: Chemistry and Pharmacology
    Notes: Two series of peptides containing L-phenylalanine, Nps-(L-Phe-L-Phe-Gly)n-OEt (n = 1-6) and Nps-(L-Phe-L-Leu-Gly)n-OEt (n = 1-7), were prepared by the fragment-condensation method using the tripeptide N-hydroxysuccinimide esters. Conformational characterization of these peptides in the solid state was performed by ir spectroscopy and x-ray powder diffraction measurement. The peptides Nps-(L-Phe-L-Phe-Gly)n-OEt take the β-structure, but the pentadecapeptide and higher peptides of Nps-(L-Phe-L-Leu-Gly)n-OEt form the α-helix, although the lower homologs take the β-structure.
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  • 194
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    Biopolymers 20 (1981), S. 2281-2283 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No. Abstract.
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    Biopolymers 20 (1981), S. 2285-2285 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 196
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    Biopolymers 20 (1981), S. 2323-2336 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a model to describe the equilibrium binding properties for the attachment of multivalent ligands to mobile receptors in membranes. The interaction is assumed to be governed by two inherently different association constants. The first of these controls the initial attachment of a ligand to its first receptor, by adsorption from bulk solution, while the second governs subsequent receptor attachments to this initially bound ligand by rearrangement of membrane-bound species. Simple statistical mechanical expressions are used to estimate contributions to these association constants that are attributable to losses of translational and rotational degrees of freedom occurring upon binding. Suitable combinatorial expressions are combined with these association constants to derive the concentrations of bound species and the binding isotherms. Examination of these expressions leads to the conclusion that once initially bound, most multivalent ligands will be completely saturated by receptors and that partially bound species will be essentially nonexistent. This behavior is attributable to the generally high overall affinities of these ligands and to the mobility of the membrane-bound species. Some specific comments are made, in light of this theory, about the binding of cholera toxin to its membrane receptor, the ganglioside GM1.
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    Biopolymers 20 (1981), S. 1413-1419 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Chitosan flakes from shrimp shells and xerogels derived from branched 1-deoxyglycit-1-yl chitosan derivatives were examined by scanning electron microscopy; the former displayed relatively large, dome-shaped orifices and the latter were found to exhibit a wide variety of ultrastructures, ranging from smooth, nonporous to microporous and microfibrillar. Some correlation between the chemical structure of the side chains of the chitosan derivatives and their microarchitecture could be established.
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  • 198
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    Topics: Chemistry and Pharmacology
    Notes: The host-guest technique has been applied to the determination of the helix-coil stability constants of two naturally occurring amino acids, L-alanine and L-leucine, in a nonaqueous solvent system. Random copolymers containing L-alanine and L-leucine, respectively, as guest residues and γ-benzyl-L-glutamate as the host residue were synthesized. The polymers were fractionated and characterized for their amino acid content, molecular weight, and helix-coil transition behavior in a dichloroacetic acid (DCA)-1,2-dichloroethane (DCE) mixture. Two types of helix-coil transitions were carried out on the copolymers: solvent-induced transitions in DCA-DCE mixtures at 25°C and thermally induced transitions in a 82:18 (wt %) DCA-DCE mixture. The thermally induced transitions were analyzed by statistical mechanical methods to determine the Zimm-Bragg parameters, σ and s, of the guest residues. The experimental data indicate that, in the nonaqueous solvent, the L-alanine residue stabilizes the α-helical conformation more than the L-leucine residue does. This is in contrast to their behavior in aqueous solution, where the reverse is true. The implications of this finding for the analysis of helical structures in globular proteins are discussed.
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  • 199
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The β-coil transition of poly(S-carboxymethyl-L-cysteine) (poly[Cys(CH2CO2H)]) and poly(S-carboxyethyl-L-cysteine) (poly[Cys((CH2)2CO2H)]) was followed by CD, potentiometric titration, and viscosity in the absence of added salt. These different properties give consistent results for poly[Cys((CH2)2CO2H)]. The CD spectra of poly[Cys(CH2CO2H)] change considerably with the degree of neutralization α even for a low-molecular-weight sample incapable of forming the β-structure. Because of the superposition of this additional effect, the dependence of CD on α is inconsistent with titration data for the case of poly[Cys(CH2CO2H)], particularly when the nπ transition is used to follow the β-coil transition. The change of CD inherent to the β-coil transition is characterized by an isodichroic point: 215 nm for poly[Cys((CH2)2CO2H)] and 218 nm for poly[Cys(CH2CO2H)]. A criterion supporting the stacking of the pleated sheet is suggested based on the isodichroic point.
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  • 200
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    Biopolymers 20 (1981), S. 1615-1623 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nature of peptide bonds in poly(aspartic acid) prepared by debenzylation of poly(β-benzyl-L-aspartate) under various conditions has been studied by means of nmr spectroscopy. It was established that the majority of the polymers prepared, as well as the commercially obtained polymer, contained aspartic acid linked in both α- and β-peptide bonds. The purest polymer, having practically undetectable amounts of β-bond, was prepared by debenzylation by HBr in trifluoroacetic acid. It was established that the β-bonds are formed via succinimides.
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