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  • Polymer and Materials Science  (6,096)
  • Ecology
  • Industrial Chemistry
  • 1980-1984  (6,121)
  • 1950-1954
  • 1935-1939
  • 1982  (3,055)
  • 1981  (3,066)
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  • 1980-1984  (6,121)
  • 1950-1954
  • 1935-1939
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  • 101
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    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1247-1260 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The physical properties of single, 5-8-μm diameter, water-swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus (G) has a value of 4.1 × 105 N m-2, the average molecular weight of chains between crosslinks is in the range of 6000-7100, and the stress optical coefficient (C′) is 1 × 10-9 m2 N-1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non-Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7-8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
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  • 102
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    Biopolymers 20 (1981), S. 1333-1335 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 103
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    Biopolymers 20 (1981), S. 1399-1411 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Heavy meromyosin binding to F-actin saturated with tropomyosin is studied theoretically. The problem is formulated as a special case of n-mer adsorption to a one-dimensional Ising lattice which is divided into m-site-long blocks.
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  • 104
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    Biopolymers 20 (1981), S. 1481-1502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio 〉 20; 0.1 〈 L/P 〈 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
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  • 105
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    Biopolymers 20 (1981), S. 1537-1547 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at 45°C and then leads to a loss of second-order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10-12% in 2.4M Et4NCl fails to increase the acceleration beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35-40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
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  • 106
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    Biopolymers 20 (1981), S. 1503-1535 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the preceding article, a Monte Carlo analysis was presented which provides a quantitative numerical relationship between the rotational diffusion coefficients, as measured by the decay of optical anisotropy following an electric field pulse, and the flexibility (persistence length) of short, wormlike chains. In the present article, the results of the foregoing analysis are applied to the observed rates of decay of birefringence for a series of sequenced DNA fragments ranging in size from 104 to 910 base pairs. Under the conditions used in this study, the DNA fragments exist as native, duplex molecules. Furthermore, conditions are defined in which the observed relaxation times are not dependent on DNA concentration, field strength, or the duration of the pulse. It is pointed out that the ionic atmosphere associated with a wormlike polyion does not exert any significant (direct) influence on the rotational diffusion of the polyion and, therefore, that the rotational relaxation times are a true measure of the configurations of the DNA molecules in solution. Moreover, excluded-volume effects are shown not to be significant for the moderately short molecules employed in this study. The major conclusion of this study is that there is no strong ionic strength dependence of the persistence length for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å. For ionic strengths significantly lower than 1 mM, electrostatic contributions to the stiffness of DNA become significant.
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  • 107
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    Biopolymers 20 (1981), S. 1575-1588 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aqueous and hydroalcoholic solutions of the heptenic macrolide amphotericin B display strong and variable signals in CD and absorption spectroscopies in the range of the π* ← π transition. An interpretation of the spectroscopic changes is proposed based on the equilibrium between two forms of the intermolecular organization: the aggregated one (A) with strong excitonic interaction and the nonaggregative one (B) whose spectra are like those of linear conjugated polyenes in true solution with a well-developed vibrational structure. The intermediate spectra are fitted by linear combination of the A- and B-form spectra. A two-level organization of the aggregates is proposed for the A-form: (1) a close packing of few molecules, which is the origin of the absorption maxima hypsochromic shift; and (2) interaction between the preceding small units inside the aggregates, which is spectroscopically expressed by the intense CD couplet.
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  • 108
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    Biopolymers 20 (1981), S. 1625-1633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polypeptides of dicarboxylic amino acids having the monomer units linked in α- and ω-peptide bonds contain two kinds of carboxyls of different acidity. How well potentiometric titration can distinguish these two carboxyls and so characterize the nature of the peptide bonds is evaluated critically. An analysis of the equation describing the dependence of pH on the degree of neutralization based on neglecting the polymer effect and a discussion of the dissociation behavior of polyanions show that the method of evaluating experimental data found in the literature is incorrect. Nevertheless, if a conformational transition does not interfere, some useful and reliable information may be gained by this method; namely, an indication of the presence of two different peptide bonds, their mole ratio, and an approximate pK value for the carboxyl of the amino acid linked in the ω-peptide bond. The presence of two types of carboxyls complicates the evaluation of the titration curves in the conformation studies.
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  • 109
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    Biopolymers 20 (1981), S. 1707-1725 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational analysis of antiparallel double-helical polynucleotides with Watson-Crick base pairing was reduced to a four-dimensional problem using original mathematical methods. In the four-dimensional conformational space the family of structures, characterized by the base-pair stacking with the most stable conformations in water solution as well as in the solid state, was localized. For the C′2-endo sugar pucker, both right-handed and left-handed structures were found; right-handed structures only, however, seem to be allowed for the C′3-endo pucker, the only possible one for ribonucleotides with base stacking.
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  • 110
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Angiotensin II and its competitive inhibitor [Sar1, Ile8]-angiotensin II, as well as several analogs of these two compounds specifically chosen for their well-defined pharmacological properties, were studied by circular dichroism and nuclear magnetic resonance methods at various pH values in aqueous solution and in d6-dimethylsulfoxide. The results were compared with their biological activities. This allowed us to establish relationships between conformation and pressor activity, explaining most of the properties of angiotensin II, its inhibitor, and the analogs successively substituted in positions 3 and 5.
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  • 111
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    Biopolymers 20 (1981), S. 2011-2020 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Peptide agonists covalently attached to tobacco mosaic virus exhibit such unusual properties as superpotency, superaffinity, enhanced resistance towards enzymic degradation, and prolonged action at the target cell. These properties can be exploited for the isolation by density-gradient centrifugation of membrane vesicles bearing specific receptors for the peptides and for radioactive and fluorescent labeling of cell-surface receptors. Our observations can be explained by cooperative-affinity phenomena caused by the deployment in space of the agonist molecules.
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  • 112
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    Biopolymers 20 (1981), S. 2035-2049 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The early steps of fibrin aggregation induced by low Reptilase concentrations were studied by means of static and dynamic light scattering. In order to obtain information on the size and shape of the first oligomers, the angular dependence of the scattered intensity and the mean Rayleigh line width were measured. Under physiological pH and ionic strength, oligomer formation was detectable immediately after enzymatic activation. Comparison of the calculated data for different models with experimental results shows that the early fibrin polymerization proceeds as an end-to-end aggregation of elongated and possibly flexible molecules approximately 75 nm long.
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  • 113
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    Biopolymers 20 (1981), S. 2083-2091 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The equivalent conductivity of salt-free solutions of deoxyribonucleates of alkali metals and ammonium obtained by filtering an isoionic DNA solution through a cation exchanger in the corresponding form has been investigated in the concentrations range of 1 × 10-4 to 4 × 10-3M. For all counterions investigated there is a linear dependence of the equivalent conductivity on \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {C_p} $\end{document}, where Cp is the nucleic phosphorus concentration. The limiting equivalent conductivity of deoxyribonucleates increases linearly with the limiting mobility of a counterion. By extrapolation to the zero mobility of the counterion, we have obtained the limiting mobility of a macroion, which is equal to 19 × 10-4 Sm m2 equiv.-1, which is in good agreement with the literature data for denatured DNA obtained by the method of a moving boundary. It is shown that the degree of binding of counterions calculated from the conductometric data in diluted DTA solutions in independent of the nature of the univalent counterion. The degree of dissociation of H+-DNA in the isoionic solution calculated with allowance for the fraction of unprotonated bases practically coincides with this value for salts of DNA. The parameter of Manning's theory calculated from the experimental data corresponds to the distance between phosphates along the chain of the macroion, which is equal to 6.7 Å. We attribute the smaller value of this distance as compared with the theoretical one for denatured DNA to the aggregation of macroions.
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  • 114
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    Biopolymers 20 (1981), S. 2165-2179 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A hydrate of cellulose II can be formed by swelling Fortisan fibers in hydrazine and then washing in water. The hydrate is stable at 93% relative humidity and has a monoclinic unit cell with dimensions a = 9.02 Å, b = 9.63 Å, c = 10.34 Å, and γ = 116.0°; the space group is P21. The unit cell contains disaccharide sections of two chains and approximately four water molecules. The structure was refined using the LALS method, based on 10 observed and 10 unobserved reflections. An antiparallel arrangement of adjacent chains was assumed, since this occurs in cellulose II (the starting material), and the hydrate also reverts to cellulose II on dehydration. Refinement of the positions and side-chain conformations of the chains shows that the chains are stacked in the same way as in cellulose II, and the hydrate is formed by insertion of water molecules between the stacks. However, all efforts to arrange the water molecules in crystallographically regular positions led to unsatisfactory agreement between the observed and calculated intensities. These results suggest an irregular arrangement of the water molecules, which was modeled using water-weighted atomic scattering factors. The analysis resulted in two refined models with relative chain staggers of ∼ +c/4 and ∼ -c/4, which are indistinguishable in terms of the x-ray agreement. Our preference is for the +c/4 model, for which the stacks of chains are analogous to those in cellulose II.
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  • 115
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of calcium ions with α-elastin has been investigated by equilibrium dialysis, CD, and microcalorimetric techniques. Consistent with literature data, it was found that the interaction in water is very poor. In trifluoroethanol (TFE), equilibrium dialysis experiments showed that calcium ions bind to ∼-elastin with an association constant of ∼250 L × mol-1. Such a figure is not consistent with highly specific, highly selective binding. It was also found that the CD response is not directly proportional to the amount of bound calcium but depends on the protein concentration. From microcalorimetric experiments it was found that the heat effect relative to the binding process is of the order of 1.9 kcal/g ion. From this figure and from the binding constant, a positive ΔS value of about 17 e.u. was evaluated, leading to the conclusion that the binding process is entropy driven. From microcalorimetric measurements a ΔH of 1.5 kcal/residue was found for the calcium-induced conformational transition of the protein.
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  • 116
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    Biopolymers 21 (1982), S. 251-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formation of polyelectrolyte complexes of glycol chitosan (GlChi) with sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) has been studied. The number of ionizable groups per pyranose ring and the degree of dissociation as a function of pH in the polycation and polyanions have been determined using conductometric and potentiometric titrations. The formation of the complexes at different pH values has been followed by turbidity measurements. It is found that stoichiometric complexes of the polycation with CMC, (GalUA)n, and AlgA are formed at a mixing ratio of 0.5, indicating that the conformation may correspond to chains of equal lengths. In the case of the complex of GlChi with DS, the stoichiometric composition corresponds to a mixing ratio of 0.62. Thin transparent films of the complexes have been obtained by dehydration under reduced pressure on a layer of mercury. The dielectric constant ε′ and loss ε″ of thin films of these complexes have been measured in the range of frequencies of 1-100 kHz at different temperatures above and below room temperature. The GlChi-DS complex shows very little change in the values of ε′ and ε″ with frequency or temperature. On the other hand, films of GlChi-CMC and GlChi-(GalUA)n complexes show a significant increase in ε′ and ε″ as the temperature is increased above room temperature. The increase is more prominent at low frequencies. This behavior is attributed to the Maxwell-Wagner interfacial polarization. In the case of GlChi-AlgA film, the values of ε′ and ε″ increase enormously as the temperature increases. This behavior is similar to the increase in ε′ and ε″ observed by Michels et al. [(1965) J. Phys. Chem. 69, 1456-1465] as the salt concentration increases in another polyelectrolyte complex studied by them. The electric double-layer mechanism proposed by Schwarz [(1962) J. Phys. Chem. 66, 2636-2642] to account for the dielectric properties of biocolloids is shown to account quantitatively for the observations on the GlChi-AlgA film.
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  • 117
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    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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  • 118
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    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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  • 119
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    Biopolymers 20 (1981), S. 129-139 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 120
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    Biopolymers 20 (1981), S. 89-109 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 121
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    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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  • 122
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    Biopolymers 20 (1981), S. 201-207 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 123
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    Biopolymers 20 (1981), S. 241-242 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 124
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 125
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    Biopolymers 20 (1981), S. 787-801 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 126
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    Biopolymers 20 (1981), S. 853-864 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 127
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    Biopolymers 20 (1981), S. 901-913 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 128
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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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  • 129
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    Topics: Chemistry and Pharmacology
    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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  • 130
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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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    Biopolymers 20 (1981), S. 891-899 
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    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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    Biopolymers 20 (1981), S. 967-975 
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    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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  • 133
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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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    Biopolymers 20 (1981) 
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  • 135
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    Biopolymers 20 (1981), S. 1113-1122 
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    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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    Biopolymers 20 (1981), S. 1147-1159 
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    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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    Biopolymers 20 (1981), S. 1261-1270 
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    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 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 20 (1981) 
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    Biopolymers 20 (1981), S. 629-632 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 141
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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 
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    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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  • 143
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    Biopolymers 20 (1981), S. 1565-1573 
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    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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    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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    Biopolymers 20 (1981), S. 1651-1669 
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    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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  • 146
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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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  • 147
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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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    Biopolymers 20 (1981), S. 1949-1958 
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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    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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  • 151
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    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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    Biopolymers 20 (1981), S. 2281-2283 
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    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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    Biopolymers 20 (1981), S. 2323-2336 
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    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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  • 156
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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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  • 157
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    Keywords: Chemistry ; Polymer and Materials Science
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    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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  • 158
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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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  • 159
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton magnetic resonance data have been obtained for 6-methyl-2′-deoxyuridine (dT*), its 3′- and 5′-monophosphates, and its 3′,5′-diphosphate, as well as for the corresponding thymine derivatives. The synthesis of the dideoxynucleoside monophosphates - d(TpT), d(T*pT), d(TpT*), and d(T*pT*) - was accomplished, and spectral data were obtained for these four dimers. The data show that the 6-methyluracil base prefers the syn conformation about the N-glycosyl bond at the monomer and dimer levels. The presence of the syn base leads to increases in the cis couplings of the sugar ring, J1′2″ and J2′3′, which indicate a trend towards eclipsing of the substituents on the C1′-C2′ and C2′-C3′ fragments. This trend is discussed in terms of changes in the pseudorotational parameters which describe the pucker of the ring. The syn base destabilizes the g+ conformer about the C4′-C5′ bond, leading to a preference for the t conformer in all dT* residues at the monomer and dimer levels. Preliminary work on the formation of cyclobutane-type photodimers in d(T*pT) and d(T*pT*) is discussed and presented as evidence for the capability of the syn 6-methyluracil base to form base-stacked complexes.
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  • 160
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    Biopolymers 20 (1981), S. 1727-1739 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete conformational analysis of B-type DNA was carried out in the independent two-dimensional surface of the hexa-dimensional conformational space of the helical structures. A theoretical double-helical model was derived by locating the deepest minimum of the conformational energy. It is similar to that obtained by x-ray refining methods; significant differences seem to be supported by relevant experimental data. Examination of the energy map allows a direct estimate of the flexibility limits of B-DNA, which are found to be consistent with a smoothly supercoiled DNA in chromatin. The structure of the hypothetical left-handed B-type DNA was predicted to be as stable as the standard right-handed model at high ionic strength. Left- and right-handed helices are, however, not interconvertible without separation of the strands, and mixing of opposite screw sense fragments is unlikely to give coaxial helices, which would prevent their packing in fibers.
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  • 161
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    Biopolymers 20 (1981), S. 1785-1791 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1. The extent of racemization and the coupling yield in peptide synthesis were studied under high dilution conditions. The azide method yielded the best results. 2. Five linear penta-peptide precursors related to gramicidin S were subjected to cyclization in order to study how the difference in the sequence influences the yield and the ratio of cyclic dimer to monomer. The azide with the sequence of -L-Pro-L-Val-L-Orn(Z)-L-Leu-D-Phe- afforded diZ-gramicidin S in a high yield of 63%. 3. Alternaria mali toxin III, a cyclotetradepsipeptide phytotoxin, was synthesized. The activated linear tetradepsipeptide containing a D-Dap(Z) (N3-Z-D-2,3-diaminopropionic acid) residue at the N-terminus afforded the cyclic precursor (53%). The Dap residue in the precursor was converted into a ΔAla residue by Hofmann degradation to give the desired product.
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  • 162
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    Biopolymers 20 (1981), S. 1761-1784 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Striking advances have been made in the synthesis of biologically active peptides. The synthesis of fully active crystalline bovine ribonuclease A by Yajima and Fujii [(1981) Biopolymers 20, 1855-1863] represents an exciting milestone. The main factors contributing to this success include sequential coupling of many small segments and a sophisticated multistage protocol for the final acidolytic cleavage of all protecting groups. However, syntheses of large peptides and proteins and even of many medium-sized peptides continue to present formidable challenges. In peptide coupling the challenge is to join large peptide segments efficiently and in good yields. For solid-phase synthesis the challenge is application of polar supports and alternative Nα-protection. With protecting groups the challenge is to achieve quantitive cleavage at the end of synthesis. Concerning racemization the challenge is to develop sensitive and rapid procedures for measuring racemization during coupling. For purification the challenge is to improve the existing procedures and to search for novel alternative separation principles.
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  • 163
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    Biopolymers 21 (1982), S. 117-129 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A melting experiment was performed on the whole set of populations of the replicative form of φX174 DNA, which can be obtained treating this DNA with rat liver nicking-closing enzyme in the presence of ethidium bromide. Gel electrophoresis performed by loading the DNA samples at neutral and alkaline pH allows separation of these populations in discrete sets of bands, which can then be compared. The outcome of the experiments indicates that in the range of electrophoretic mobilities which can be explored, no band is formed exclusively by circular complementary strands which can be separated by alkaline denaturation. These results are compared with what would be expected if double-stranded closed circular DNA had structures other than the canonical double helix. Under nonrestrictive hypotheses, the experiments reported allow one to obtain a minimum estimate of the absolute value of the linking number of a closed circular double-stranded DNA: for native φX174 RF DNA, the linking number appears to be greater than 12 (in absolute value). Some data on the electrophoretic mobility of denatured closed circular duplexes are reported, which still wait for a physicochemical interpretation.
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    Biopolymers 21 (1982), S. 169-179 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthetic cyclic octapeptides of general structure cyclo[Glu(γOBzl)-Sar-Gly-(N-R)Gly]2 (R = n-hexyl and cyclohexyl) transport calcium ions selectively across organic phases and phospholipid membranes. We have now used proton nmr spectroscopy (360 MHz) to study the solution conformation(s) of their calcium complexes. When Ca(ClO4)2 was added to solutions of these peptides in CDCl3, nmr spectra of the resulting calcium complexes were characteristic of a single C2-symmetric conformer. From a Karplus-Bystrov analysis of vicinal coupling constants in both the peptide backbone and Glu side chain (treated as an ABCC′MX spin system), in conjuction with model-building studies, a structure was proposed in which the calcium ion is bound in an octahedral-type complex by the four (coplanar) carbonyl groups of the (all-trans) Glu-Sar and Gly-(N-R)Gly peptide bonds. Occurrence of preferred rotamers about Glu side chain Cα-Cβ bonds indicated that restricted rotation in peptide side chains arises upon calcium binding.
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  • 165
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    Topics: Chemistry and Pharmacology
    Notes: Attachment of the side-chain carboxyl of the protected aspartic or glutamic acid ester to the resin support has been established for the solid-phase synthesis of the asparagine or glutamine peptide. After further elongation of the α-amino deprotected resin-bound peptide ester with protected peptide fragments and the final detachment from the resin support by ammonolysis, the larger peptides containing, or preferably C-terminated with, asparagine or glutamine could be obtained. Thus, the C-peptide of human proinsulin was prepared by coupling to the resin-bound dipeptide derivative, Leu-Glu(OCH2Ph®)·OtBu, with six fragments consecutively. It was obtained in an overall yield of 36% after detaching from the resin with alcoholic ammonia, followed by mild acidolysis, DEAE cellulose chromatography, and gel filtration. This procedure has now been applied to the synthesis of the C-terminal fragment of the insulin A chain ending in asparagine, and also to the synthesis of the threonine or serine peptide, where the anchorage to the resin was designed by the reaction of the sidechain hydroxyl with succinic anhydride in the presence of 4-dimethylaminopyridine to form the hemiester of succinic acid, which in turn was condensed to the aminomethyl resin by the DCC-HOBt procedure. Model experiments on the synthesis of the Z-Thr(CO-CH2CH2CONHCH2Ph®)·OtBu and Bpoc-Lys(Boc)-Thr(COCH2CH2CONHCH2Ph®)·OtBu, as well as their detachment from the resin by amminolysis or hydrazinolysis, have shown the potential for a milder process in the solid-phase synthesis of larger peptides.
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    Biopolymers 20 (1981), S. 1913-1920 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: β-Turns are a common feature of cyclic peptides, but judging from recent x-ray and solution studies of cyclic hexapeptides it is not always possible to predict in advance the type of turn and the position of the turns in the sequence. Two or more backbone conformations containing β-turns may be of comparable energy and in rapid solvent- and temperature-dependent equilibrium in solution. The use of differential relaxation effects produced by a nitroxyl radical to locate β-turns with only minor perturbation of such equilibria is noted. Examination of the effect of a nitroxyl on the N-H resonances of the decapeptide hormone luteinizing hormone releasing hormone supports a dominant conformation with a β-turn at Gly6-Leu7. Although this turn is probably part of the biologically active conformation, it is not obvious in the more active [D-Ala6] analog.
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  • 167
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    Topics: Chemistry and Pharmacology
    Notes: A quinoxaline antibiotic triostin A has a bicyclic octadepsipeptide structure. Proton and carbon-13 nmr spectra showed the presence of two symmetrical conformations favoring polar and nonpolar solvents, respectively. They interconvert slowly on the nmr time scale, and this slow interconversion is due to the cooperative effects of the presence of the quinoxaline ring and the N-methyl peptide bonds. Reversal of the chirality of the disulfide bond as the origin of the slow exchange was excluded by the presence of two conformers for S-benzyltriostin A. Conformer 2, which favors the polar solvent, can form hydrogen-bonded complexes with purine nucleoside derivatives in organic solvents, but conformer 1 does not. The binding sites were elucidated and a mode of interaction with DNA proposed.
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    Biopolymers 20 (1981), S. 2001-2010 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: There is a general parallelism in the strategy followed in the design of hormonal peptide analogs and protease inhibitors. However, in the latter, one more dimension has been added with the development of mechanism-based inhibitors, a dimension that is not yet available for hormonal peptides because of the lack of knowledge about receptor mechanisms. The recently advanced concepts of transition state and bi-product analogs have made possible the development of highly potent active-site directed reversible protease inhibitors of great therapeutic potential.
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    Biopolymers 20 (1981), S. 2021-2031 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two-dimensional nmr techniques have been carried out for the peak assignment of the spectrum of a somatostatin analog. Two-dimensional J-resolved spectroscopy simplified the rather broad and complicated spectrum to show the center of chemical shifts of each resonance and gave information on the coupling profiles. Another technique, two-dimensional spin-echo correlated spectroscopy, revealed the connectivities between protons which are correlated by weak spin-spin couplings. The combination of the results of these two complementary techniques made it possible for us to assign almost all peaks of the spectrum of the 11-residue somatostatin analog.
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    Biopolymers 20 (1981), S. 2093-2120 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard-particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi-spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self- and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi-spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme-catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self-association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self-association of larger macromolecules.
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    Biopolymers 20 (1981), S. 2143-2163 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements have been made on the flow dichroism of T7 DNA as a function of NaCl concentration. In high salt, our results are compatible with an optical factor of -1.4 and a persistence length of 470 Å. The former is in agreement with expectations from the x-ray diffraction structure of fibrous B-DNA, and the latter is in the midrange of recent determinations. As salt concentration is decreased, the persistence length increases. The relation of our study to other recent investigations and with current theories of the electrostatic contribution to persistence length is discussed. We note that the separation of the electrostatic expansion factor into long- and short-range effects is somewhat arbitrary and might affect the interpretation of different experimental results in different ways. Finally, our hydrodynamic factors are consistent with a chain which is partially free-draining. This goes against the traditional interpretation but is in agreement with two recent observations.
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  • 172
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    Topics: Chemistry and Pharmacology
    Notes: The conformations of a pentapeptide L-His-L-Arg-L-Trp-Gly with weak adrenocorticotropin (ACTH) activity and its analogs, where each L-amino acid residue is substituted by D-residue, were investigated by means of proton and carbon-13 nmr spectroscopy on their DMSO-d6 solutions. The spectra indicated the presence of slowly exchangeable conformation isomers for D-Phe and D-Arg analogs, due to steric hindrance around the arginine residue. The activation energy of the hindered rotation of the arginine side chain was estimated to be more than 19 ∼ 20 kcal/mol. Spin-lattice relaxation times of carbon-13 nuclei also indicated slow segmental motion of the arginine side chain of the D analogs. An effect on proton chemical shifts by intermolecular electrostatic interaction between the arginine side chain and the C terminal carboxylic residue was observed. We did not observe, however, a direct correlation between pentapeptide activity and molecular conformation at this stage of the experiments.
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  • 173
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    Topics: Chemistry and Pharmacology
    Notes: Simultaneous curve fitting for the ionization parameters of oxidized and reduced horse heart cytochrome c in 0.15M KCl and 20°C yields values for the ionization constants (as pK′) and the heats of ionization (ΔHi) which can reconstruct either the potentiometric or thermal titration curves. Reduced cytochrome c requires 8 sets of groups, whereas oxidized cytochrome c requires 10 sets of groups. The additional groups in the oxidized preparation appear to involve the ferriheme (pK′, 9.25; ΔHi, 13.7 kcal/mol) and a tyrosine (pK′ ≃ 10.24) that is not present in the reduced form. The potentiometric and thermal difference curves (reduced - oxidized) involve the appearance of 17 kcal/mol centered at pH 9.7 and 5.8 kcal/mol centered at pH 4.9. The carboxyl groups in both species appear to be normal for the hydrogen-bonded form. Only one histidine has normal ionization properties (pK′, 6.7; ΔHi, 7.5 kcal/mol), as do 17 of the lysine residues (pK′, 10.8; ΔHi, 11.5 kcal/mol).
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 20 (1981), S. 2369-2380 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Transient electric birefringence measurements of the rotational diffusion constant of five short restriction fragments of the plasmid pBR322 show that the hydrodynamic length is independent of sodium ion concentration in the range of 0.2 to 2.5 mM. The fragments are too stiff to be modeled as wormlike molecules. The rotational relaxation times of the fragments, which range from 64 to 124 base pairs, have been used to calculate the rise per base pair using six different theoretical expressions for the length dependence of the rotational diffusion coefficient of straight cylinder. The best estimate for the rise per base pair of Na-DNA in solution is 3.3 ± 0.1 Å.
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 20 (1981), S. 2509-2531 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamic parameters for the double-strand formation of the molecules rCAmG + rCUnG, m,n = 5-7, and dCAmG + dCTnG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo-oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA7G·rCU7G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double-strand formation are discussed.
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    Biopolymers 20 (1981), S. 2635-2648 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An azo pyrimidine nucleotide has been prepared and enzymatically attached to oligo(A) primers. The nucleotide's azo pyrimidine group has previously been shown to initiate polymerization of methacrylate esters designed to bind marker groups for visualization by microscopy. When attached to RNA molecules complementary to a chromosomal DNA segment, these nucleotides may allow localization of the DNA segment following in situ hybridization of the probe, methacrylate polymerization, and marker attachment. Since mRNA molecules of potential interest as probes bear a 3′-poly(A) tail, the modified nucleotides were added to oligo(A) primers as models. First, N4-ureidocytosine nucleotides were enzymatically added to ApApA, (Ap)9A, or [5′-32P]-(pA)10, using the modified cytidine 5′-diphosphate and “primer-dependent” polynucleotide phosphorylase (M. luteus). In the case of the ApApA-primed reaction, the N4-ureidocytosine nucleotides in the product polynucleotide were converted into azo nucleotides by oxidation with N-bromosuccinimide. The other two primers were employed to study the time course of polynucleotide formation and to verify that primer was indeed being utilized by the enzyme. The suitability of the modified nucleotide for in situ hybridization studies was examined. Poly(N4-ureidocytidylic acid) was prepared from poly(C) and semicarbazide by the bisulfite-catalyzed transamination reaction. It was found that 95% of the N4-ureidocytosine nucleotides in this polynucleotide survive the elevated temperatures typically required for DNA:DNA denaturation and RNA:DNA annealing. When poly(N4-ureidocytidylic acid) was mixed with poly(I) in buffered aqueous salt solutions, no evidence for hybridization was found, so binding of the probe RNA to the denatured chromosomal DNA molecule via the modified nucleotides is not expected. Upon oxidation of poly(N4-ureidocytidylic acid) with N-bromosuccinimide, the azo nucleotides were formed, as judged by the appearance of a characteristic peak at approximately 350 nm in the uv-absorption spectrum of the yellow-orange product, azoRNA. The azo nucleotides in azoRNA exhibited the expected acid lability, which is known to be accompanied by 1-glyceryl methacrylate polymerization in the case of the simple azo pyrimidine. Because 1-glyceryl metharcylate bears substituent glycol groups for attaching heavy atoms or fluorescent markers, it is possible that probe RNA molecules bearing azo nucleotides may be useful for localizing low-multiplicity genes along eukaryotic chromosomes.
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    Biopolymers 20 (1981), S. 2671-2690 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We show that the persistence length a of DNA, derived from total intensity laser light scattering of linear Col E1 DNA and corrected for excluded-volume effects, varies from about 68 nm in 0.005M NaCl to about 40 nm in 0.2M NaCl, leveling off to a constant value (about 27 nm) at high NaCl (1-4M) concentration. These observations do not agree with current views on the effect of electrostatic charge and ionic conditions on DNA dimensions. The apparent diffusion constant Dapp, determined from laser light scattering autocorrelation as a function of scattering vector q, at NaCl concentrations 0.005-4M, correctly yields the translational diffusion coefficient Dt at low values of q and scales with molecular dimensions rather than segment length at high values of q; thus, Dapp/Dt yields a universal curve when plotted against q2Rg2, where Rg is the radius of the gyration. The sedimentation coefficients s at 0.1 and 0.2M NaCl concentration closely agree with the well-tested empirical relations, and a combination of s, Dt, and the appropriate density increments yield correct molar masses over the whole salt concentration range. Approximate constancy of DtRg indicates limited draining in translational flow. We present some observations and thoughts on the regimes in which a dependence of the correlation decay times on q3 rather than q2 applies. We conclude that quasielastic laser light scattering discloses little information about dynamics of internal motion of DNA chains.
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    Biopolymers 21 (1982), S. 25-42 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (L-Cys)n + N-base systems and (L-Cys)n + (L-Lys)n systems were studied by ir spectroscopy. It is shown that in the water-free systems, SH⃛N ⇌ S-⃛H+N hydrogen bonds are formed. With the (L-Cys)n + N-base systems, both proton-limiting structures in the SH⃛N ⇌ S-⃛H+N bonds have equal weight when the pKa of the protonated N-base is 2 pKa units larger than that of (L-Cys)n. The same is true with the water-free (L-Cys)n + (L-Lys)n system. Thus, with regard to the type of proton potentials present, these hydrogen bonds are proton-transfer hydrogen bonds showing very large proton polarizabilities. This is confirmed by the occurrence of continua in the ir spectra. Small amounts of water open these hydrogen bonds and increase the transfer of the proton to (L-Lys)n. In the (L-Lys)n + N-base systems, with increasing proton transfer the backbone of (L-Cys)n changes from antiparallel β-structure to coil. In (L-Cys)n + (L-Lys)n, the conformation is determined by the (L-Lys)n conformation and changes depending on the chain length of (L-Lys)n. Finally, the reactivity increase in the active center of fatty acid synthetase, which should be caused by the shift of a proton, is discussed on the basis of the great proton polarizability of the cysteine-lysine hydrogen bonds.
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  • 181
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    Biopolymers 21 (1982), S. 101-116 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report electric-dichroism and electron-microscopic studies of chromatin fibers fixed by protein-protein crosslinking at salt concentrations ranging from 10 to 100 mM. The results confirm a progressive disorganization of the fiber as the salt concentration is lowered. The positive dichroism and large polarizability anisotropy characteristic of the 300-Å diameter fiber found in 100 mM salt are replaced by negative dichroism and smaller effective polarizability anisotropy or dipole moment for samples fixed at lower salt concentration. We interpret the results in terms of segmental, field-induced orientation of the disorganized structure which is present in low salt concentrations. We also observed a field-induced absorbance decrease in chromatin fibers fixed at salt concentration at and below 100 mM. All three optical effects, namely overall orientation of the high-salt fixed fiber, segmental orientation of the low-salt fixed fiber, and field-induced absorbance decrease, occur on roughly the same time scale, 20-100 μs for 50 nucleosome polynucleosomes. The polarizability anisotropy of fibers fixed in 100 mM salt was found to be proportional to the length of the fragment and to the reciprocal square root of the conductivity of the solution used for electric-dichroism measurements. Addition of Mg2+ to the measurement buffer affected the dichroism amplitude of samples fixed below 100 mM salt but not those fixed at 100 mM salt. The results reinforce the need for caution in interpreting electric-dichroism measurements on chromatin fibers because of possible field-induced distortion effects.
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  • 182
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    Biopolymers 21 (1982), S. 219-232 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA with Mn2+ as the only counterion has been prepared, and the extent of the Mn2+ binding was determined under a variety of conditions through measurements of the proton relaxation enhancement of water. The total extent of Mn2+ binding per DNA phosphate is found to be 0.43 ± 0.04, independent of the metal ion concentration in the experimental range of 2.8 × 10-5 to 2.1 × 10-3M. The predictions of Manning's condensation theory and those obtained from solution of the generalized Poisson-Boltzmann equation regarding the extent of divalent ion binding to polyelectrolytes, in the presence and absence of monovalent counterions, are compared with one another and with the experimental results. Good agreement between the two theoretical approaches is found, with less than 14% variance in the predicted extent of binding over a large range of mono- and divalent ion concentrations. While the predictions of both theoretical approaches generally agree with the experimental results, some discrepancies are noted and their possible origins discussed.
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  • 183
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    Biopolymers 21 (1982), S. 1275-1300 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The basic formulas for the incorporation into the diffusion-collision model of the stabilities of intermediate states on the folding pathway are derived and discussed. A hypothetical two-step folding pathway is calculated in detail. A model for the production of incorrectly folded intermediates is suggested and some numerical estimates made. Implications and future directions in the evolution of the model are discussed. Three appendices deal with some mathematical aspects of the model.
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  • 184
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quasielastic light scattering and electrophoretic light scattering experiments were performed on chicken erythrocyte polynucleosome solutions at various temperatures and ionic strengths. The apparent diffusion coefficient, Dapp, was found to depend on the scattering vector K. In general, Dapp can be described as a damped oscillatory function of K in the ionic strength range of 10 to 60 mM and over the temperature range of 10 to 40°C. Electrophoretic light scattering studies on total digest chromatin samples indicate the apparent charge on the polynucleosomes increases as the ionic strength is lowered from 10 to 1 mM. These data are interpreted in terms of fluctuations in the surface charge distribution of the polyion and subsequent inducement of an asymmetric distribution of small ions about the polyion. These fluctuation components lead to the formation of “clusters” of polyions.
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  • 185
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    Biopolymers 21 (1982), S. 1399-1410 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Absorption of radiation by DNA polymer is calculated for the case of bent polymer chains. The molecule is assumed to be straight except for localized bends. The region between two bends is studied in particular. The vibrational properties of the bends are parameterized by a transmission and a reflection coefficient. A general Green function expression for absorption is studied for various values of the damping rate, as well as the transmission/reflection coefficients. Curves of absorption vs frequency are shown for a number of cases.
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  • 186
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: When adsorbed from an aqueous dilute solution at high pH into the pores of an inert cellulose acetate filter, poly(α,L-glutamic acid) remains strongly anchored to the pore walls. The existence of the helix-coil transition for the adsorbed polypeptide in a certain pH range is evidenced by static and dynamic membrane properties displayed by the “activated” filter, such as excess cation uptake, membrane potential, and hyraulic permeability. In particular, the variations of the hydrodynamic thickeness present a sigmoidal shape characteristic of the helix-coil transition at the interface, a transition apparently less sharp than in solution.
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  • 187
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    Biopolymers 21 (1982), S. 343-358 
    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 linear dichroism (LD) of rat liver chromatin oriented by flow. Soluble chromatin, prepared by brief nuclease digestion, is found to exhibit a positive LD at low ionic strength (1 mM NaCl), with a constant LD/A over the absorption band centered at 260 nm (A, isotropic absorbance). Several previous dichroism studies on soluble chromatin have been performed on sonicated materials and have given negative LD, probably due to the presence of uncoiled DNA. The positive dichroism can be interpreted in terms of a supercoil of DNA in chromatin with a pitch angle larger than 55°, and is, for example, consistent with a model where the cylindrical nucleosome core particles are stacked face to face in the chromatin filament. In contrast to the nuclease-digested chromatin, sonicated chromatin was confirmed to exhibit negative LD. This difference can be attributed to a partial uncoiling of the linker regions between the nucleosomes due to the shearing. The structural transition of chromatin to a compact form can be observed as a reduction of the positive LD of the nuclease-digested chromatin to almost zero in 0.1 M NaCl or in 0.1 mM MgCl2. This transition is due to a decreased electrostatic repulsion between negative phosphate groups on the DNA chain. In the case of Na+, this can be explained as a screening effect due to the bulk concentration of Na+. With Mg2+ a considerably stronger effect may indicate a more localized binding to the phosphates. At ionic strengths higher than 0.5M NaCl, the dissociation of the histones from DNA leads to uncoiling of chromatin. The change in LD during this process shows that histone H1 contributes only to a small degree to the coiling of the DNA chain, whereas histones H3 and H4 play the major role in the coiling.
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  • 188
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: On the basis of measurements of enthalpy of dissociation and of dilution, an interamolecular conformational transition induced by pH change is shown for pectic acid in aqueous solution. Additional evidence is given by potentiometic, viscometric, and chiroptical results. The transition from a more rigid, probably H-bonded, structure prevailing at low pH to a more extended one at around neutrality is accompanied by a ΔH value of about 500 cal/equiv and a ΔS value of 1.6 cal/equiv K in water at 25°C. The addition of salts increases the stability of the rigid conformation without changing the general features of the phenomenon. Dilatometric measurements suggest that the transition is accompanied by practically no change in the overall solvation of the polymer chain.
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  • 189
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    Biopolymers 21 (1982), S. 459-470 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amphotericin B, a polyene macrolide antibiotic, exists in aqueous solution as a poorly soluble, high-molecular-weight aggregate. A borate complex of this polyene was prepared that has greater solubility and is less aggregated. In aqueous solution this borate complex exists as a mixture of several molecular species differing in borate content, molecular weight, and molecular conformation. The solubility varied with pH and was minimal at neutrality. Throughout the pH range it was one to two orders of magnitude higher than that of the parent compound. The molecular size distribution, as determined by differential ultrafiltration, showed a progressive increase in the weight fraction of aggregates going from acid to alkaline solutions. The sizes of aggregates ranged from under 25 to over 100 molecules. The borate content of the complexes increased with increasing pH. No borate was complexed in acid solutions. This indicated that amphotericin B and borate ions can complex to form copolymer chains of varying length in which these species alternate, since both are bifunctional. The complexation equilibrium is favored by high pH. Absorption and CD spectra indicated that the polyene molecules can stack reversibly to form dimers. Dimerization constants calculated from the spectra were highest in neutral solution and declined with increasing acidity or alkalinity. In alkaline solutions the polymer chains are long and extended, with minimal stacking. In neutral solution the chains are shorter and extensively stacked. In acid solutions no borate complexes are formed, and the polyenes are stacked to an intermediate degree. The very different effects of pH and concentration on the degree of complexation with borate and on the degree of dimerization of the polyenes shows that these equilibria are independent of each other.
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  • 190
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    Biopolymers 21 (1982), S. 601-610 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A major component of pigment gallstones (PS) is a black, insoluble substance. It has been suggested that this pigment material might be a highly crosslinked polymer, and if such were the case, it should imbibe solvent (swell) to the maximum permitted by the crosslinks of its macromolecular network. We measured the equilibrium amount, qeq, by which pulverized, desiccated PS swells in different liquids, including isotonic aqueous buffers at pH values from 1.5-11.5. For ionic strengths ≥ 0.15, the dependence of qeq on pH exhibits a broad titration curve with a midpoint near pH 7. qeq was 〈 1.2 in methanol, dimethylformamide, dimethylsulfoxide, and chloroform. The ir absorbance from vinyl groups in the black pigment was only one-eighth that of unconjugated bilirubin, the primary chemical building block of PS; this implicates vinyl groups in the formation of a polymer network. The rise in qeq with increasing pH suggests that the carboxyl groups are free to ionize and are therefore not involved in the covalent bonds that make the crosslinked polymer. A network polymer structure would account for the inability to dissolve PS in those solvents in which unconjugated bilirubin is soluble.
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  • 191
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    Biopolymers 21 (1982), S. 653-664 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 25Mg-nmr data are reported that address the nature of the magnesium ion-DNA interaction. It is found that competitor ions such as calcium, mercury, zinc, and cobalt ions are not effective in competing for all of the magnesium ion-DNA interaction that is reported by the 25Mg-nmr spectrum. The temperature dependence of the 25Mg-nmr spectrum in DNA solution studied at high concentrations of competitor ion indicates that the chemical-exchange lifetime of the magnesium ions at DNA binding sites makes a major contribution to the 25Mg-nmr line width. However, the activation parameters are not consistent with the temperature dependence of either transport properties or chemical exchange with phosphate groups alone, but are consistent with a sum of at least two processes that provide opposing contributions to the 25Mg-nmr relaxation. It is also shown that the non-Lorentzian character of the 25Mg-nmr line previously reported is consistent with the effect of an incompletely averaged static nuclear electric quadrupole interaction and/or an exchange process that is slow with respect to the magnitude of this interaction. Because the concentrations employed in these experiments are high, the present data do not provide a direct or critical test of the electrostatic theories of ion-polyelectrolyte interaction. The present data do demonstrate, however, that such theories alone are insufficient as a basis for understanding the 25Mg-nmr data.
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  • 192
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    Biopolymers 21 (1982), S. 703-704 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 193
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    Biopolymers 21 (1982), S. 715-728 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The persistence length of lugworm cuticle collagen in 0.1M acetic acid was evaluated as 1600 ∼ 1800 Å by Yamakawa-Fujii's model for a wormlike chain from the sedimentation constant and the intrinsic viscosity. The persistence length was further examined for a series of sample “collagen sonicates” produced by varying the duration of sonic irradiation. To estimate the salt effect on the persistence length, measurements were made over a range of NaCl concentrations from 0 to 0.1M. The results showed that the cuticle collagen and collagen sonicates had identical values of persistence length and that the neutral salt effect for the cuticle collagen was far smaller than that for DNA.
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  • 194
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    Biopolymers 21 (1982), S. 797-804 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used translational diffusion coefficient measurements and subunit hydrodynamic theory to determine the dimensions and shape of bacterioophage T4D baseplates and tails. The diffusion coefficient of the baseplate, measured by quasielastic laser light scattering (QLS), was determined previously by Wagenknecht and Bloomfield to be D = 8.56 × 10-8 cm2/s. For the tail, we found D = 5.88 × 10-8 cm2/s by QLS, and D = 6.02 × 10-8 cm2/s by combining sedimentation coefficient and molecular weight in the Svedberg equation. These values, which have an uncertainty of ±2.7%, when combined with subunit hydrodynamic theory, enabled us to refine estimates of dimensions obtained by electron microscopy. For the hexagonal baseplate, the vertex-to-vertex distance is about 480 Å, the thickness is 160 Å, and there are six extended short fibers 320-Å long and 40 Å in diameter. When a baseplate of these dimensions is attached to a tail tube-sheath-connector complex 1050-Å long and 240 Å in diameter, the calculated D is 5.93 × 10-8 cm2/s, within 1% of experiment. This combined use of electron microscopy and hydrodynamics, using the former to ascertain shape, and the latter to obtain solution dimensions, is a powerful approach to the structure of biomolecular complexes.
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  • 195
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly(L-lysine) of various molecular weights between 2700 and 475,000 was spin-labeled. From the electron spin resonance spectra, the degree of freedom of the nitroxide was determined by calculation of the rotational correlation time as the poly(L-lysine) underwent the pH-induced random coil to α-helix conformational transition. In general, the rotational correlation time of the nitroxide increased as the pH was increased, indicating a more restricted environment for the spin label when poly(L-lysine) is deprotonated. For the high-molecular-weight poly(L-lysine) this corresponds to the formation of the α-helix and indicates that the side chain-side chain interaction and decreased segmental motion of the backbone (slightly) restricts the motion of the spin label. For the 2700-molecular-weight poly(L-lysine), previously shown not to assume a helical conformation at high pH, the increase in the rotational correlation time of the spin label indicates that the side chain-side chain interaction takes place after deprotonation but without helix formation. This may indicate that helix formation per se is not needed to produce the observed effect even with the high-molecular-weight polymers. The rotational correlation time of the spin label at a particular pH did not depend on the molecular weight of the poly(L-lysine) over the 200-fold range of molecular weights. This indicates that the rotational correlation time reflects the rotational mobility of the spin label in a localized environment and not the rotational diffusion of the entire macromolecule.
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  • 196
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of fluoroquinacrine, 3-fluoro-7-chloro-9-(diethylamino-1-methylbutyl-amino)acridine, with poly(A), DNA, and tRNA has been investigated by monitoring changes in the 19F-nmr properties, the fluorescence, and the optical absorbance of the drug. The changes in the properties of fluoroquinacrine in the presence of nucleic acids are similar to those observed for quinacrine and suggest that the drugs bind in a similar fashion. The molecular dynamics of fluoroquinacrine bound to nucleic acids were determined by interpreting the data from a number of different nmr relaxation experiments with a two-correlation-time model. The two motions are the long-range bending motion of the drug-nucleic acid complex and the sliding of the drug between the base pairs. Both dipolar and chemical shift anisotropy contributions to the nmr relaxation parameters were taken into consideration. The binding of fluoroquinacrine to tRNA appears to be different from that observed for binding to DNA. Optical absorbance and 19F-nmr were also used to examine the helix-to-coil transitions of the drug-nucleic acid complexes. In the DNA complex, the 19F chemical shift changes parallel the absorption changes that occur during the transition. 19F-nmr and absorption show that the drug-tRNA complexes undergo a cooperative helix-to-coil transition, with the drug binding sites melting when the tRNA is 70% denatured.
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  • 197
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    Biopolymers 21 (1982) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 198
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    Biopolymers 21 (1982), S. 1971-1977 
    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 the title compound, a model for the glycosyl linkage between the asparagine side chain and N-acetyl glucosamine in glycoproteins, has been determined and compared to other model structures. The pyranose ring in the crystal is in the 4C1 chair conformation and the amide functions at C1 and at C2 are both oriented such that the amide protons are nearly trans to their respective sugar-ring protons. Coupling constants determined from the fully assigned proton nmr spectrum in aqueous solution are consistent with the conformation in the crystal.
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  • 199
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    Biopolymers 21 (1982), S. 1991-2010 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Flow linear dichroic studies have been conducted on phage T4B in its fast and slow forms. The behavior of the phages is well represented by an equivalent ellipsoid model using the Peterlin-Stuart theory. The measurements permit the evaluation of the optical factor of the DNA in the phage and the rotary diffusion coefficient of the phage particle. Both these quantities change during the slow-fast conversion. The rotary diffusion results are in good agreement with those obtained by other workers with other methods. The optical factor is negative, indicating a net alignment of DNA helices parallel to the phage axis. The results exclude certain simplified models for the packaged DNA but do not lead to a unique structural conclusion. The flow dichroism experiment and its interpretation are described, and a simple method of calculating optical factors for complicated but cylindrically symmetric structures is presented.
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  • 200
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has recently been proposed that the repeating backbone nucleotide may be regarded as consisting of two blocks of equal magnitude representable by two virtual bonds. Implicit consideration of the nucleotide (ψ,ψ) and internucleotide (ω′,ω) geometry that generate variety in polynucleotide conformations, and of the constancy of the repeating structural moieties (P-C4′ and C4′-P) independent of the above rotations, has enabled us to utilize this scheme in the study of ordered structures such as di-, oligonucleotides and, most significantly, tRNA. The polynucleotide folding dictated by short-, intermediate-, and long-range interactions in the monoclinic and orthorhombic forms is described and compared through circular plots depicting the virtual bond torsions and distance plots constructed independently for backbone as well as bases. The torsions and the bond angles associated with the virtual bonds afford a clear distinction between ordered helical segments from loops and bends of tRNA. Lower virtual bond torsions (-60° to 60°) concomitant with higher values of virtual bond angles characterize various bend regions, while torsions around 160°-210° typify ordered helical strands. The distance plot elucidates the type of interaction associated with various sub-structures (helix-helix, helix-loop, and loop-loop) that form the constituents of different structural domains. Several other features such as the manifestation of the P10 loop and the approximate twofold symmetry in the tRNA molecule are conspicuous on the distance plot.
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