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  • Polymer and Materials Science  (4,992)
  • Humans
  • 1995-1999
  • 1980-1984  (3,365)
  • 1970-1974  (1,970)
  • 1925-1929
  • 1983  (3,365)
  • 1970  (1,970)
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  • 1995-1999
  • 1980-1984  (3,365)
  • 1970-1974  (1,970)
  • 1925-1929
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  • 1
    Electronic Resource
    Electronic Resource
    Ionic polysaccharides. IV. Free-rotation dimensions for disaccharide polymers. Comparison with experiment for hyaluronic acid (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 811-824 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The root-mean-square end-to-end distance has been calculated for a model allowing free rotation about glycoside bonds for the general case of polysaccharides having a disaccharide repeating unit. Numerical estimates are given for several naturally occurring structures based on an idealized pyranose unit in the C1 chair conformation. Extrapolation procedures which make use of the intrinsic viscosity [η] in good solvents to obtain unperturbed dimensions do not represent, data for hyaluronic acid very well, especially at low molecular weights. However, order-of-magnitude estimates suggest that this polymer behaves similarly to other polysaccharides, and probably has stiffer local structure than typical non-ionic synthetic polymers. A double logarithmic plot of the product of [η] and M̄w, the weight-average molecular weight, against the degree of polymerization in the range for M̄w of 104 to 2 × 104 permits a straight-line fit of available data for all the glycosaminoglycans, including heparin and the chondroitin sulfates, as well as sodium carboxymethyl cellulose. This result suggests similarity of short-chain hydrodynamic behavior of these polymers.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090707
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  • 2
    Electronic Resource
    Electronic Resource
    The 4th Jerusalem symposium (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 875-875 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090711
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  • 3
    Electronic Resource
    Electronic Resource
    Masthead (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090801
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  • 4
    Electronic Resource
    Electronic Resource
    Diffusional boundary spreading in the ultracentrifuge (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 865-874 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A common approximation for deriving solutions to the Lamm equation is to neglect diffusion. This paper presents a singular perturbation technique that allows one to estimate the band spreading due to nonzero diffusion coefficient. We illustrate the general mathematical technique by its application to sedimentation when pressure effects are important. Comparison of the approximate solution with accurate numerical solutions shows that the relative errors are of the order of 1% both for concentration and concentration gradient for parameters of chemical interest.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090710
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  • 5
    Electronic Resource
    Electronic Resource
    Role of pH in charging of glycogen (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 891-896 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Glycogen acquires a negative charge in both alkaline and acidic solutions and can move in an electrical field, its mobility being related to the degree of alkalinity or acidity. There is a slight increase in relative viscosity at both ends of the pH spectrum. These effects and the changes in nuclear magnetic resonance as a function of pH are interpreted.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090803
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  • 6
    Electronic Resource
    Electronic Resource
    Studies on the viscosity of solutions of bovine liver glutamate dehydrogenase and on related hydrodynamic models; effect of toluene on enzyme association (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 877-889 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The viscosity of bovine liver glutamate dehydrogenase solutions was studied at 10 and 20° C in 0.2.M sodium phosphate buffer at pH 7, in the concentration range 0.1-8 mg/ml. A method for the study of the viscosity of very dilute solutions of associating enzymes is described. It was found that the reduced specific viscosity ηsp/c of glutamate dehydrogenase continuously increases with increasing enzyme concentration, from about 4 ml/g at the lowest concentrations to about 16 ml/g at 8 mg/ml. In the presence of 10-3M GTP and 10-3M NADH the viscosity increase is much smaller and the results can be extrapolated to zero enzyme concentration to yield an intrinsic viscosity [η] = 3.2. The values of ηsp/c in phosphate buffer alone apparently extrapolate to the same value of [η], or to a value close to it. We also observe that, in the presence of toluene ηsp/c increases very much more with enzyme concentration: ηsp/c already equals 16 ml/g at a concentration of 0.75 mg/ml. These observations are in good agreement with the hypothesis that the active oligomer of glutamate dehydrogenase (MW = 312,000) associates with increasing enzyme concentration to form linear rodlike polymers of indefinite length. This association is strongly diminished by the addition of 10-3M GTP, 10-3M NADH. Toluene, on the other hand, promotes reversible association to linear polymers of very high molecular weight. The transverse and axial rotary frictional coefficients of macroscopic bodies, similar to a physical model for the structure of glutamate dehydrogenase recently advanced, were determined. Assuming that the viscosity of the model is equal to that of an ellipsoid of rotation with identical frictional coefficients, we calculate [η] = 3.26 ml/g according to Kuhn and 3.20 ml/g according to Simha, for the glutamate dehydrogenase oligomer, in good agreement with the result derived from the study of enzyme solutions.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090802
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  • 7
    Electronic Resource
    Electronic Resource
    Surface chemistry of poly(β-beiizyl L-aspartate) (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 911-922 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular monolaycrs of poly(β-benzyl L-aspartate) spread at. an air-water interface have been studied. The results obtained both by direct observations on the monlayer and from examination of collapsed films with polarized infrared spectroscopy and electron diffraction are consistent with the presence of right handed α-helices in the mono-layer when the molecular weight is high. When 1% (v/v) isopropanol is present in the subphase the right-handed helix prevails, provided that the monolayer is first spread on water. Monolayers of low molecular weight polymer appear to form the crossed-β structure. Orientated collapsed films of high molecular weight polymer can be converted to the left-handed α-helical and to the ω-conformation, and the mechanisms are discussed. The surface chemistry of this polymer is compared with that of related polymers and a consistent pattern of behavior emerges.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090805
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  • 8
    Electronic Resource
    Electronic Resource
    Characterization of acid-denatured DNA by low-angle light scattering (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1017-1028 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Low-angle light scattering results reported previously demonstrated that measurements on high molecular weight native DNA must be made at angles below 30° in order to obtain correct molecular weights. Earlier light-scattering data obtained on denaturated DNA at angles above 30° showed no change in molecular weight upon denaturation, even though other techniques clearly showed that strand separation occurred. This paper reports low-angle measurements on solutions of calf thymus and T7 DNA denatured under acidic conditions. The results demonstrate that a halving of molecular weight consistent with strand separation is detected by light scattering only when low-angle data are used to obtain correct molecular weights for native material. As expected from theoretical considerations, the scattering from denatured DNA is a linear function of sin2(θ/2), where θ is the angle of observation. This result shows that anticipated experimental artifacts have no significant effect on the low-angle measurements and demonstrates that the curvature in the scattering envelope observed for native DNA below 30° is an inherent property of the native molecule.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090905
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  • 9
    Electronic Resource
    Electronic Resource
    Kinetics for the transition between cis- and trans-helices in poly-L-prolineA preliminary report of this work was presented at the 156th National Meeting of the American Chemical Society, Atlantic City, New Jersey, September 1968. (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1001-1016 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics for the cis-trans isomerization of long-chain poly-L-proline has been studied as a function of pressure, temperature, and solvent composition in the acetic acid + n-propanol solvent system. Our complete kinetic curves were fitted by Monte Carlo techniques, and rate constants for nucleation, growth, and termination were estimated. It was found that for the formation of a cis-helix, high pressure, low temperature, and increased acetic acid content of the solvent, lowered the rate of nucleation relative to growth. The inverse seems to be t rue for the formation of a trans-helix. Molecular models suggest that this behavior of the kinetic constants can be due to the exposure of peptide units to solvent in the transition state for trans nucleation, and the burying of peptide units in the transition state for cis nucleation. It is further suggested from our analysis of complete kinetic curves that at least one of the assumptions usually made in the analysis of relaxation kinetics is invalid for poly-L-proline.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090904
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  • 10
    Electronic Resource
    Electronic Resource
    X-Ray diffraction of ethylenediamine-amylose complex (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1039-1047 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solutions of amylose in ethylenediamine yield a crystalline film complex upon evaporation of solvent. The x-ray analysis indicates the presence of a tetragonal-shaped cell with a symmetry approximating that of space group P212121. The amylose sixfold helix has a diameter of 13.3 Å and a translation period of 8.0Å. Chemical and physical analyses support a complexing ratio of one ethylenediamine molecule to every two glucose units. The structure is nearly identical to any amylose-dimethyl sulfoxide complex previously examined. The square mode of packing arrangement appears to result from complexation between amylose chains. Such complexing indicates a much greater degree of amylose interaction than is observed in amylose complex structures having a hexagonal close-packing arrangement.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1970.360090907
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  • 11
    Electronic Resource
    Electronic Resource
    Potentiometric titration of poly-S-carboxymethyl-L-cysteine in aqueous NaCl solution (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1049-1058 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: pH titration measurements of poly- S-carboxymethyl-L-cysteine were undertaken in the aqueous Nacl solution in relation to the β form-random coil transition. The titration curves show a marked molecular weight dependence because of the shortened chain length of materials. Comparison of the optical rotatory dispersion parameter a0 with the titration curve reveals that the titration curve apparently reflects a β structure-random coil transition. The β form of this polymer is assumed to be an intramolecular β form, rather than a β structure stabilized by an intermolecular hydrogen bond, at least in the polymer concentration range considered here. The standard free energy change per amino acid residue for the transition from un-ionized random coil to un-ionized β form is estimated to be about -750 cal/mole residue in the range of 0.005-0.2M NaCl concentration.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090908
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  • 12
    Electronic Resource
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    Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1059-1077 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism (CD) spectra of the four usual deoxymononucleosides, all sixteen deoxydinucleotides, and a number of trinucleotides have been measured. The dimer spectra are quite different from the sum of the spectra of their constituent monomers. This indicates the presence of base-stacked conformations analogous to those found for ribonucleoside diphosphates. The CD spectra of several deoxytrinucleotide diphosphates and single-strand f 1 DNA can be calculated fairly well by using a semi-empirical nearest-neighbor approach. There is little or no effect of terminal phosphate or of salt concentration on the optical properties of most deoxy oligomers. The possibility of simultaneous analysis of mixtures of deoxypurine or deoxypyrimidine sequence isomers has been examined. This seems to be a viable approach for the analysis of purine runs but cannot promise much success for pyrimidine runs.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090909
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  • 13
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    Oligonucleotide interactions. IV. Conformational differences between deoxy- and ribodinucleoside phosphates (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1079-1103 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism spectra of all 16 ribodinudeoside phosphates containing the bases adenine, uracil, cytosine, and guanine have been measured at room temperature and neutral pH. These results are compared with the circular dichroism spectra of the corresponding deoxy compounds. From the optical properties it is clear that the geometry of the base-stacked conformation of ribo compounds must differ substantially from that of deoxy compounds. Because of this, it is not possible to draw firm conclusions about the relative extent of stacking in most ribo and deoxy compounds. The optical rotatory dispersion of about a dozen deoxy and ribodinucleoside phosphates has been studied as a function of temperature. These results confirmed the conclusions drawn earlier from measurements at a single temperature. Several dinucleoside phosphates containing a 2′ → 5′ phosphodiester bond have also been examined. These compounds have a substantial degree of base stacking at room temperature. The geometry of the stacked conformation is different from that of either the normal ribo dimer or the deoxy dimer. The role of the 2′-hydroxyl group in stabilizing base stacked geometries has been examined by studies on C-2′-O-methyl-pC. This compound has optical properties almost identical to those of CpC. This suggests that the effect of the 2′ hydroxyl is felt indirectly through its perturbation of the geometry of the sugar ring rather than directly by hydrogen bonding. It is not possible at present to identify precise conformational differences among deoxy-, ribo-and 2′ → 5′ ribodinucleoside phosphates.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090910
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  • 14
    Electronic Resource
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    Aggregation of poly-L-proline II (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1119-1124 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090912
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  • 15
    Electronic Resource
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    The influence of single-strand breaks on the kinetics of denaturation of DNA (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1349-1360 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The influence of single-strand breaks on the kinetics of the relaxation of DNA in a solution of low ionic strength has been investigated by a temperature jump method. The relaxation of DNA after a jump of 0.7 °C in the melting region has been monitored by measuring the extinction at 260 nm. For essentially monodisperse T4 DNA (M = 130 × 106) two distinct relaxation times have been observed, that depend markedly on the initial extent of denaturation 1 - θ. The larger relaxation time decreases from 450 sec to about 300 sec, the smaller one from 55 see to 30 when 1 - θ increases from 0.03 to about 0.8. The dependence of these relaxation times on the average number of single-strand breaks per molecule (p) appears to be very small up to p = 100. However, the relative contribution of the slow process decreases sharply when p increases from 0.6 to 30 and remains nearly constant for larger p. The observations are discussed in the light recent theories of the kinetics of denaturation.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360091105
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  • 16
    Electronic Resource
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    Electro-optic scattering studies on deoxyribonucleic acid (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1361-1372 
    Details
    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 of the intensity of light scattered from aqueous solutions of calf thymus DNA with and without the application of electric fields. For fields approaching 150 V/cm and frequencies below 2.5 KHz, changes (ΔI) of up to 10% in the residual scattered intensity were observed. In agreement with previous dielectric and electric birefringence measurements, a low frequency dispersion of ΔI was observed, from which a rotary diffusion constant (D) of 1200 s-1 was determined. Interpreting the electric field data in terms of the classical dipolar orientation theory led to values of 2.4 × 10-25 cm (7.4 × 10-14 esu) and 4.3 × 10-25 cm (13 × 10-14 esu) for the permanent dipole moment and the anisotropy of the electric polarisabilities respectively. Furthermore the permanent dipole moment was along the major molecular axis and the particles orientated in the field as rigid entities. The zero field data indicated a molecular shape which was not rodlike but corresponded to the Kratky-Porod “stiffness” parameter of x = 24 for the wormlike coil model. Although curved, the molecules appeared to orientate in low-intensity electric fields as rigid, but not rodlike molecules. The implications of this on recent discrepancies in D determined by two or more dynamic relaxation methods is briefly discussed.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360091106
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  • 17
    Electronic Resource
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    Buoyant density and solvation of magnesium DNA (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1391-1402 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The buoyant density of T-4 DNA was determined by equilibrium sedimentation in a density gradient, of mixed solutions of cesium and magnesium chlorides and bromides. The preferential hydration was calculated from these data, allowing appropriately for the exchange equilibrium of DNA with Cs+ and Mg++ ions. The charge and intrinsic solvation of the counterions were found to have no appreciable effect on the hydration of the DNA, the extent of solvation depending only on the thermodynamic, activity of the water. Various reasonable hypotheses are discussed to account for these results.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360091108
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  • 18
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    Studies on bacteriophage MS2. VIII. Evidence for dimer formation of MS2 RNA by reaction with formaldehyde at acidic pH (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1373-1389 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reaction of 27 SMS2 RNA with formaldehyde normally results in an unfolded, 13.4 S form. At acidic pH, however, and under the proper ionic conditions, a compact component sedimenting at 36-40 S was obtained. The molecular weight of this species corresponds to a dinner. The formaldehyde concentration was not critical, and approximately the same number of base pairs had been opened in the compact and in the unfolded form. Presumably dimers, which had been specifically formed under defined conditions, were stabilized by formaldehyde-induced crosslinks. Similar dimers were formed by 16 S and by 23 S ribosomal RNA, but not by tRNA.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1970.360091107
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  • 19
    Electronic Resource
    Electronic Resource
    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220101
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  • 20
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    Theory of protein secondary structure and algorithm of its prediction (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 15-25 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long-range interactions between different regions, incorporating all these interactions in a single Ising-like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α- and β-structures for different residues in synthetic polypeptides, while long-range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x-ray structural data became available.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220105
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  • 21
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    Monte carlo simulations of peptide solvation (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 27-31 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To increase our understanding of peptide-water interactions, we are simulating the behavior of water molecules in the intermolecular channels of [Phe4Val6]antamanide dododecahydrate crystals. There is good overall agreement between the positions predicted using two alternative potential functions and those that have been observed by x-ray diffraction. Detailed differences between the predictions for the two potential functions are discussed.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220106
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  • 22
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    An empirical approach to protein conformation stability and flexibility (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 49-58 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220110
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  • 23
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    Conformational properties of microtubule protein: Their relation to the self-assembly process in vitro (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 87-91 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Near- and far-uv CD spectra of microtubule protein preparations have been examined to study the possible role of protein conformation in relation to the kinetics of the self-assembly of these proteins into microtubules in vitro. Although tubulin can form conformations with high helical content under apolar solution conditions, this transformation is apparently not involved in self-assembly. There is no major perturbation of tubulin near-uv CD by reagents and solution conditions favoring assembly. Thus, in these preparations, tubulin, as dimer and as oligomer with MAPs, is effectively in the conformation in which it undergoes self-assembly. This conclusion is consistent with a hybrid model of assembly of microtubule protein involving direct incorporation of oligomeric species as an alternative to the condensation polymerization of tubulin dimer as the exclusive assembly mechanism.
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    The unfolding mechanism of thermolysin (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 101-105 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ligand-modulated kinetics of the autoproteolysis of thermolysin and the high-molecular-weight products of the reaction provide evidence for the conclusion that separation of the two structural domains is most probably the first step on the unfolding pathway of the protein under native conditions.
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    Genetic and biochemical analysis of in vivo protein folding and subunit assembly (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 125-129 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The in vivo pathway of folding and subunit assembly of a trimeric bacteriophage protein has been studied by characterizing precursors to the native protein and by analyzing temperature-sensitive mutations that kinetically block the pathway. The native trimer is formed via an intermediate composed of three partially folded chains, the protrimer. At 39°C, temperature-sensitive mutations prevent the formation of both the native trimer and the protrimer, possibly by destabilizing earlier intermediates. However, the mutations do not affect the stability of the native protein, formed at 30°C. Thus, these mutations identify amino acid residues involved in interactions that determine the folding pathway.
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    Conformational and functional properties of hemoglobin in perturbed solvent: Kinetics of O2 release (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1677-1696 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of O2 release by oxyhemoglobin caused by sodium dithionite, in the presence and in the absence of organic cosolvents (monohydric alcohols and formamide) at 10°C. This study was performed by using standard stopped-flow techniques coupled with microprocessor-based data acquisition. We have fitted the experimental data to a mathematical expression obtained on the basis of a two-state model that takes into account the kinetic heterogeneity between α- and β-chains and the presence of αβ-dimers in oxyhemoglobin solutions. Results indicate that the cosolvents mainly affect the allosteric parameter L, i.e., the T ⇄ R conformational equilibrium of hemoglobin, leaving the intrinsic deoxygenation rates of both R and T states almost unaltered. The L values obtained in the present work are in excellent agreement with analogous values previously estimated from oxygen equilibrium measurements.
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    Solution properties of porcine submaxillary mucin (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1657-1675 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Porcine submaxillary mucin (PSM) is a glycoprotein composed of a protein core and frequent, short oligosaccharide side chains. We report static and dynamic light scattering experiments and intrinsic viscosities for PSM in aqueous solvent systems. In 0.1M NaCl solution, the data suggest PSM exists as large, internally branched, highly hydrated, polydisperse aggregates that slowly dissociate to give a stable species of weight-average molecular weight (Mw) 7.4 × 106. In 6M GdnHCl solution, the noncovalent bonds between PSM molecules are broken, giving a highly elongated molecule of Mw = 2.0 × 106. The irreversible nature of this dissociation suggests that the forces that stabilize the native aggregates of PSM in 0.1M NaCl are specific in nature. On reduction of PSM with mercaptoethanol, the polydispersity decreases and Mw also decreases to 9 × 105. A discrete change is observed in the solution properties of PSM in 0.1M NaCl at a concentration of 2mg/mL, manifested by a sudden decrease in the translational diffusion coefficient, an increase in viscosity number, and a decrease in slope of the osmotic compressibility. We tentatively propose that a weak and reversible secondary association process occurs at this concentration, although a purely hydrodynamic interaction cannot be ruled out.
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    Linear dichroism studies of nucleic acids. III. Reduced dichoism curves of DNA in ethanol-water and in poly(vinyl alcohol) filmsFor Part II in this series, see Matsuoka, Y. & Nordén, B. (1982) Biopolymers 21, 2433-2452. (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1731-1746 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The uv linear dichroism of calf thylus DNA has been studied at different degrees of orientation both in flow-oriented ethanol-water solutions and in a stretched aqueous host of poly(vinyl alcohol) (PVA). The reduced dichroism (LDR) curves in the region 250-290 nm for DNA in PVA films at 75 and 100% relative humidity (r.h.) are in fair agreement with the curves calculated for the A- and B-forms of DNA, based on the fiber structures and the π-π* transitions of the free bases. This suggests that DNA adopts its A and B conformations in PVA at 75 and 100% r.h. In ethanol, on the other hand, a deviation from the A-form spectrum shows that the conformation of DNA in the solution can differ from the fiber structure. At shorter wavelenghts, a positive contribution to LDR is explained in terms of an out-of-plane polarized n-π* transition.
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    Localized vibrational modes at a double-helix-single-strand junction (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1759-1767 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A vibrational analysis has been performed for a double-helix-single-strand junction. A Green's function technique has been used in treating the junction as a defect on an otherwise perfect system of infinite chain homopolymers. We calculate that the hydrogen-bond stretching at the junction is amplified by a factor of two relative to the interior of the double helix, B poly(dG)-poly(dC). Breathing modes localized near the junction have also been predicted at 77 and 94 wave numbers. The calculated results are shown to be consistent with predictions from recent nmr studies.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360220801
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    Nmr studies of a free and protected tetrapeptide glycyl-L-prolylglycylglycine in β-turn-supporting environment (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1853-1868 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Nmr studies of the protected and free tetrapeptide Gly-Pro-Gly-Gly were carried out in β-turn-supporting solvents, that is, in CDCl3 for Z-Gly-Pro-Gly-Gly-OMe and in Me2SO-d6 for H-Gly-Pro-Gly-Gly-OH. Comparisons with specifically α-deuterated analogs gave complete assignments of the NH and methylene regions. Analysis of chemical shifts, coupling constants, and the temperature dependence of chemical shifts show that the peptide adopts a type II β-turn conformation. This turn is stabilized for the protected tetrapeptide by two hydrogen bonds between (i) C=O (Gly1) and NH(Gly4), and (ii) urethane function NH and methyl ester C=O.
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    Computer simulation of the conformational properties of retro-inverso peptides. II. Ab initio study, spatial electron distribution, and population analysis of N-formylglycine methylamide, N-formyl N′-acetyldiaminomethane, and N-methylmalonamide (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1901-1917 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio minimal and split-valence basis set calculations have been performed on compounds that are involved in retro-inverso modifications, i.e., gem-diaminoalkyl and malonyl structures. These calculations are compared with empirical force field calculations and the minor differences discussed. All calculations agree that the preferred helical conformation of the isolated gem-diaminoalkyl and malonyl derivatives of residues found in the retro-inverso modified peptides is 5-8 kcal/mol lower than the Ceq7 conformation preferred by the isolated peptide residues. Population analysis and contour plots of the charge distribution are used to help explain the differences between the model compounds.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360220901
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360220601
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    Lysinium, argininum, glutamate, and aspartate ions in water solution (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1449-1460 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: SCF-LCAO-MO ab initio calculations were carried out for the interaction between a charged amino acid and a water molecule. The results obtained were fitted by an analytical potential function of the atom-atom type, and the corresponding potential surfaces were examined by means of orientationally optimized isoenergy contour maps. Monte Carlo simulations were also carried out on a few selected solute-water clusters at T = 300 K, in order to obtain insight into the solvation structure.
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    Improved technique for calculating X-ray scattering intensity of biopolymers in solution: Evaluation of the form, volume, and surface of a particle (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1507-1522 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An improved cube method has been developed for calculating the intensity of diffuse x-ray scattering of macromolecules in solution using a certain set of their atomic coordinates. The technique is based on the ideas of B. Lee and F. M. Richards [(1971) J. Mol. Biol. 55, 374-400] and Richards [(1977) Annu. Rev. Biophys. Bioeng. 6, 151-176] on the possibility of estimating the molecular and accessible surface of a particle by “rolling” a sphere, simulating a water molecule, on its molecular surface. It is shown that this technique is more advantageous than earlier versions of the cube methods. The improved technique for calculating scattering curves was utilized for several globular proteins, and for the first time, reliable scattering curves were obtained for protein-“bound” water complexes. In the case of globular proteins and tRNA, this technique has permitted a strict evaluation of their accessible surfaces, their volumes, and, apparently for the first time, their complete molecular surfaces.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360220701
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    Viscometric study of the proteoglycan-hyaluronate (2:1) “dimer”: Minimum hyaluronate chain length (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2501-2506 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360221203
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    Extended retro-inverso analogs of somatostatin (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2523-2538 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extended retro-inverso modification was introduced at the central six residues of the somatostatin molecule, the region of internal enzymatic degradations. The synthesis of the analog [Ala4,g-Phe6-r-D-Phe7-r-D-Trp8-r-D-Lys9-r-D-Thr10-m-R,S-Phe11]-somatostatin required a unique strategy accommodating the unusual structure. Side-chain protection based on the t-butyl group in combination with Fmoc and Nps α-amino protection was employed. The key component containing the gem-diaminoalkyl residue was generated by an iodobenzene bistrifluoroacetate-mediated reaction. The separation of diastereomers of the cyclic tetradecapeptide in highly pure form was accomplished by high-performance liguid chromatography on a semipreparative scale. The analogs exhibited very low potency in the growth hormone inhibition test in vitro. This is interpreted as the consequence of the complex structural changes created by the extended retro-inverso modification.
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    A critical evaluation of models for complex molecular dynamics: Application to NMR studies of double- and single-stranded DNA (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2703-2726 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nature of internal and overall motions in native (double-stranded) and denatured (single-stranded) DNA fragments 120-160 base pairs (bp) long is examined by molecular-dynamics modeling using 13C-nmr spin-relaxation data obtained over the frequency range of 37-125 MHz. The broad range of 13C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T1 values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double-stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τx = ∼10-6 s;τZ = ∼1.8 × 10-8s), which is in good agreement with values calculated from hydrodynamic theory (τx = ∼1.8 × 10-6 s; τZ = ∼2.7 × 10-8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual C—H vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τw = ∼4 × 10-9 s, θcone = ∼21°) or as a bistable jump (τA = τB = ∼2 × 10-9 s, θ = ∼15°). We discuss the critical role in molecular-dynamics modeling played by the angle (β) that individual C—H vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τW = ∼0.2 × 10-9 s, θcone = ∼50°), and overall motion is affected by becoming essentially isotropic (τx = τZ = ∼5 × 10-8 s) for the single-stranded molecules. Since 13C-nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.
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    Kinetic studies of the interaction of methyl orange with poly(L-lysine) by stopped-flow with circular dichroism detection (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2035-2044 
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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 methyl orange with poly(L-lysine) was studied kinetically by the stopped-flow technique with CD detection, as well as by static CD titration experiments. In the static experiments, the differences observed in the polymer-to-dye ratio dependences of the CD spectra and absorption spectra suggested at least two kinds of bound states of the methyl orange attached to the polymer. The kinetic experiments using the stopped-flow apparatus, however, revealed four distinct reaction processes. The reaction mechanism was elucidated from the concentration dependence of the time constant for each process as follows: the first process was attributed to the bimolecular binding step of methyl orange to the side chain of poly(L-lysine), the second and third process were ascribed to the intramolecular reaction of the polymer-dye complex, and the fourth process was found to be the intermolecular aggregation of the polymer-dye complex. The origin of the stacking of methyl orange on poly(L-lysine) is discussed on the basis of the characteristics of signal amplitudes obtained from the kinetic experiments for these processes.
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    Comparative study of GuHCl denaturation of globular proteins. I. Spectroscopic and chromatographic analysis of the denaturation curves of ribonuclease A, cytochrome c, and pepsinogen (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2105-2122 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Novel devices for the spectroscopic and chromatographic analysis of the denaturation curves of the protein are described. A multidimensional spectroscopic measuring system makes it possible to carry out simultaneous and continuous acquisition of a set of data of different spectroscopic dimensions at several wavelengths in the course of increasing or decreasing denaturational perturbation. GuHCl-gradient chromatography can provide information about the progressive change of the protein volume in the course of increasing GuHCl concentration. Thus, denaturation curves with a high data-point density can be obtained. The data-storing function by a magnetic disk memory provides enough precision for a rigorous investigation of the correlation among the curves that probe different aspects of denaturation. The GuHCl denaturation of RNase A, cytochrome c, and pepsinogen are studied to demonstrate the high performance of these devices. Three types of transitions are found in these three proteins and the multiphasic nature of the transitions is clearly detected in the last two proteins.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360221001
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    Quantitative relationship between the surface charge density and dynamic charge of linear polyelectrolytes in the low charge-density limit (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2169-2172 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Boundaries of the universal K3 region and plateau region of the dynamic structure factor for DNA (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2207-2217 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A sufficiently long semiflexible filamentous macromolecule is theroretically expected to exhibit three different domains of behavior of its apparent diffusion coefficient Dapp(K) as a function of scattering vector K: (1) the small wave vector limit, where Dapp(K) = D0 is the translational diffusion coefficient of the center-of-mass; (2) the universal K3 region, where Dapp(K) = (kBT/6πη)K is a universal function of K independent of any property of the molecule itself; (c) the plateau region at large K2, where Dapp(K) approaches either a plateau, or gradually sloping quasiplateau, characteristic of local (elastic) rigid-body motions of the filament. The existence of each of these different domains has now been established experimentally for at least some polymers. The boundaries of the universal K3 region and the plateau region are determined theoretically here using precise quantitative criteria for universal or plateau behavior of Dapp(K) for a Rouse-Zimm model containing N + 1 subchains with rms subchain extension b. Allowing a maximum of 13% nonuniversal behavior, the domain of the universal K3 region is given by K2R2G = K2Nb2/6 ≥ 7 and K2b2 ≤ 0.54. Allowing as much as 10% nonplateau behavior, the boundary for onset of plateau behavior is K2b2 = 18.3. Dapp(K) is at least 50% nonuniversal when K2b2/6 = 6 ln 3. Extension of these results to DNA is examined theoretically, and good agreement of the pertinent predictions with published experimental data is demonstrated.It is concluded that no truly universal K3 region exists for DNA with Mr ≤ 107 and persistence length a ≥ 450 Å, although marginally (≤17% nonuniversal) universal behavior, is exhibited in a very narrow domain 0.64 × 1010 ≤ K2 ≤ 0.84 × 1010 cm-2 for φ29 DNA (Mr = 11.5 × 106). More than 50% of Dapp(K) is governed by local (elastic) rigid-body motions when K2 = 5.23 × 1010 cm-2. The existence of a very wide region of nonuniversal apparent K3 behavior extending up to very large K2, far into the plateau region, is demonstrated in a plot of Dapp(K)/K vs K2 for the Rouse-Zimm model. This is shown to stem in part from visual artifacts of plotting Dapp(K)/K vs K2, even for rigid species.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360221101
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    Orientational interactions in low-concentration DNA solutions (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2353-2366 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rotational relaxation tiem τ3 of DNA molecules (Mw ≃ 5 × 106) in solution has been determined by the transient electric birefringence method. The analysis of the birefringence decay makes it possible to study only the higher-molecular-weight fraction, the molecules being considered as rigid elongated particles in a short time scale. A marked concentration dependence of the relaxation time has been observed for DNA in low ionic strengths. Above a critical concentration c*, τ3 increases with the DNA concentration, c. The value of c* increases with the ionic strength. For 10-3 ionic strength (with NaCl), c* is about 10 μg/mL; then we observe the same strong concentration dependence of rotational relaxation times as recently reported for rodlike M-13 viruses [Maguire, J. F., McTague, J. P. & Rondelez, F. (1980) Phys. Rev. Lett. 45, 1891-1894]. These results may be discussed in terms of the Doi-Edwards theory for rotational relaxation time of rigid macromolecules [Doi, M. (1975) J. Phys. 36, 607-611; Doi, M. & Edwards, S. F. (1978) J. Chem. Soc. Faraday Trans. 74, 918-932] and the critical concentration above which the interactions between the molecules begin to appear allows determining the corresponding molecular length. We observe a very good agreement between the DNA lengths obtained from the c* values and by using the infinite dilution value of τ3 and Broersma's equation. Therefore, only highly diluted solutions can be used if intrinsic molecular properties based on the rotational diffusion of high-molecular-weight elongated molecules are studied.
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    Heat capacity increments: Conformational transitions in polypeptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2411-2421 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A thermodynamic treatment of the helix-coil transition of synthetic polypeptides in binary organic solvent mixtures is extended to describe isobaric heat-capacity increments associated with the phenomenon. This development resolves such increments into three components: two associated respectively with intrinsic differences between the ordered and disordered states of the macromolecule and between the coil-solvent complex and its components, and a third term derived from the temperature dependence in the fraction of coil residues bound to active solvent. Insights derived from this analysis are also applied to the discussion of some heat capacity increments associated with the denaturation of globular proteins.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Laser-Raman spectra, sulfhydryl groups, and conformation of the cystine linkages of β-lactoglobulin (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2507-2511 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    X-Ray diffraction studies on the structure of hydrated collagen (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2539-2547 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The temperature dependence of the humidity-sensitive spacing, d, related to the lateral packing of collagen molecules was measured for fully hydrated collagen. In the vicinity of 0°C, a sudden change in d was observed, which was reversible with temperature. In the diffraction profile, below 0°C, a set of diffraction peaks identified with the hexagonal crystalline form of ice was observed. With the reduction in water content, the intensity of the set of diffraction peaks decreased and was found to be zero at a water content of 0.38 g/g collagen. These results were considered to be caused by the frozen water in collagen fibril below 0°C. According to the water content dependence of d, it was considered that up to a certain water content water absorbed would be stowed in the intermolecular space of collagen and above that water content water molecules would aggregate to make pools, i. e., extrafibrillar spaces. The unfreezable bound water was considered to be located in the intermolecular space of collagen. Size of the extrafibrillar space, determined from the intensity analysis of a smallangle x-ray scattering pattern, corroborates the speculation that the water showed in the extrafibrillar space is freezable and free. The formation of the hexagonal crystalline form of ice in the extrafibrillar space was considered to cause the sudden change in d at 0°C.
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    Volume changes accompanying thermal denaturation of deoxyribonucleic acid. II. Denaturation at alkaline pH (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 445-457 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The change in apparent molal volume φ of DNA on thermal denaturation in carbonate buffer at pH 11.0 has been determined by the dilatometric method. It was found that φ increases sigmoidally during the helix-coil transition. Several methods, including a colorimetric technique that closely simulates the conditions used in the dilatometric experiments, were employed to estimate the protons lost by the DNA during the transition. These measurements indicated that the extent of the proton loss depends on the counterion present, increasing in the order Li+ 〈 Na+ 〈 K+ 〈 Cs+. The major part of the volume changes observed during the denaturation is due to the volume changes expected to accompany the transfer of protons from the bases guanine and thym ne to carbonate ions. As has been previously reported for the denaturation of DNA at neutral pH, the volume change directly due to the change in shape of the polymer molecules is so small as to be experimentally undetectable.
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    Location of proline derivatives in conformational space. II. Theoretical optical activity (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 569-588 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The coupling of theoretical optical calculations with experimental data provides a check of the validity of the theory or provides conformational information. The theory was validated by studies in which the approximate conformation was located independently. These studies have shown that a theory restricted to the two lowest energy transitions for each chromophore gives qualitative agreement with experiment. On the other hand, for some of the proline derivatives, the theoretical treatment allows detailed conformational assignments. Both successes and failures in correlating theory with experiment are discussed. The results presented provide a basis for assessing the prospects for relating protein and polypeptide optical activity to their conformations.
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    Ethidium bromide-DNA complex: Wavelength dependence of pyrimidine dimer inhibition and sensitized fluorescence as probes of excited states (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 639-653 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: Ethidium bromide inhibits the formation of ultraviolet-induced pyrimidine dimers in DNA. The efficiency of dimer inhibition increases with increasing energy of the exciting photons. The efficiency of energy transfer from the DNA singlet to the dye singlet, as monitored by sensitized fluorescence, is independent of wavelength. The efficiency of singlet-singlet transfer agrees with that for dimer inhibition at photon energies corresponding to excitation of the lowest singlet state of DNA. Our results support a model in which dimers are formed both directly from the singlet state and also from the triplet state, with triplets arising from higher vibrational levels of the singlet.
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    Testing of A size criterion for DNA-hydrocarbon binding (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 689-696 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The intercalation model of DNA-hydrocarbon binding appears reasonable, but rests on indirect evidence only. To test the model, a size criterion for binding has been proposed. The size criterion is based on the assumption that hydrophobic forces play a major role in the binding of hydrocarbons to DNA. It states that hydrocarbons which are small enough to intercalate into DNA and be well protected from contact with the medium, will be found to bind to DNA; those that are too large will not. We report results on the binding of fourteen polycyclic aromatic hydrocarbons to DNA. Predictions based on the size criterion were found to be valid in all cases tested.
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    Cooperative binding of adenosine by polyuridylic acid: A further analysis (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 697-715 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The dialysis data of Huang and Ts'o for the cooperative binding of adensine to polyuridylic acid are analyzed here using a grand-partition function Ising model method similar to that originally employed for polyelectrolytes by Rice and Nagasawa. An appropriate modification permitting the treatment of the sliding degeneracy of the two polyuridylic acid strands is also included. In addition to the previously estimated stacking energy of about -6 kcal/mole one also obtains the free energy change F̄ for the transfer of a single adenosine molecule from a fixed site in solution to a fixed site on the polyuridylic acid. This binding energy falls in the range F̄ = -140 to +620 cal/mole, indicating that binding in the 1:2 (purine: pyrimidine) complex is either very weak or repulsive. The absence of any comparable cooperative stacking of adenosines in solution at the same concentration together with the likely repulsive character of the binding implies that the stacking energy must contain a significant contribution from other processes than simple stacking of adenosines. A generalization of the theory to treat multicomponent binding and longer-range interactions is effected, and the form applicable to simultaneous binding of both adenosine and guanosine by polyuridylic acid is presented.
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    PMR chemical shifts of TFA in poly(γ-benzyl L-glutamate) solutions (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 739-744 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The present communication describes a new way of studying helix-random coil transformations of polypeptide, poly-(γ-benzyl L-glutamate), in benzene-trifluoracetic acid (TFA) and chloroform-TFA systems. The difference between the PMR chemical shift of TFA with and without the polypeptide, measured as Δ, may be used to follow the conformational transition. This technique is particularly useful for concentrated solutions, where the PMR peaks of the polymer are so broad that no valuable information may be derived. As the TFA content increases in the system (at constant polymer concentration), Δ decreases normally whether the polymer is helical or random. However, Δ changes in a different way in the helix-random coil transition region, and actually increases with increasing TFA content. This peculiar behavior is explained in terms of the solvation of the helix and random coil structures.
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    NMR study of the slowly exchanging hydrogens of 640 Å steerskin collagen (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 745-748 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    Solution properties of synthetic polypeptides. VI. Helix-coil transition of poly-N5-(3-hydroxypropyl)-L-glutamine (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 717-738 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new procedure for evaluating u and σ characterizing σ-helix-forming polypeptides in solution was derived from Nagai's theory for the helix-coil transition of such polymers. Here u is the activity for helix formation from random coil, and σ is the helix initiation parameter. The necessary data are the helical content fN at fixed solvent and temperature as a function of N, where N is the degree of polymerization of the polypeptide sample. Such data were obtained from ORD measurements on a number of fractionated samples of poly-N5-(3-hydroxypropyl)-L-glutamine (PHPG) in mixtures of water and methanol covering the complete range of composition and at various termperatures (5-40°C). When analyzed in terms of the proposed procedure, they yielded values of σ which were in the range (3.2 ± 0.6) × 10-4, substantially independent of solvent composition and temperature. These values were much larger than those obtained recently for σ of poly(β-benzyl-L-aspartate) in m-cresol and in a mixture of chloroform and DCA. The data for [η] and s0 (limiting sedimentation coefficient) as functions of molecular weight indicated that the molecular shape of PHPG in pure methanol is essentially rodlike, whereas that in pure water is not entirely randomly coiled but rather may be regarded as an interrupted helix. These indications were consistent with the results from ORD measurements. When plotted against the corresponding values of fN, the values of [η] and [s0] for PHPG in mixtures of water and methanol of various compositions and temperatures formed smooth composite curves, and we attributed these phenomena to the fact that σ of PHPG was nearly constant under these solvent conditions. Here [s0] stands for a reduced limiting sedimentation coefficient which is equal to the inverse friction factor of the solute molecule.
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    Masthead (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Interaction of nucleic acids. VI. Interaction of purine with nucleic acids (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 765-782 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The interaction of purine with DNA, tRNA, poly A, poly C, and poly A. poly U complex was investigated. In the presence of purine, the nucleic acids in coil form (such as denatured DNA, poly A and poly C in neutral solutions, or tRNA) have lower optical rotations. In addition, hydrodynamic studies indicate that in purine solutions the denatured DNA has a higher viscosity and a decreased sedimentation coefficient. These findings indicate that through interaction with purine, the bases along the poly-nucleotide chain are unstacked and are separated farther from each other, resulting in increased assymmetry (and possibly volume) of the whole polymer. Thus, the de-naturation effect of purine reported previously can be explained by this preferential interaction of purine with the bases of nucleic acids in coil form through a hydrophobic-costacking mechanism. Results from studies on optical rotation and helix-coil transition show that the interaction of purine is greater with poly A than with poly C. The influence of temperature, Mg++ concentration, ionic strength, and purine concentration on the effect of purine on nucleic acid conformation has also been investigated. In all these situations the unraveling of nucleic acid conformation occurs at much lower temperatures (20-40°C lower) in the presence of purine (0.2-0.6M).
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    Configurational statistics of polysaccharide chains. Part II. CelluloseContribution No. 286 from Centre of advanced study in physics, University of Madras, India. (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 783-790 
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    Notes: The characteristic ratio of unperturbed cellulose chain was computed as a function of the angle τ at, the bridge oxygen atom and the degree of polymerization. Very high values of the order of 40 or more, depending on the angle at the bridge oxygen atom, have been obtained for this ratio, indicating that cellulose chains are highly extended. The average dimensions of cellulose chains are found to be sensitive even for small changes in the angle at the bridge oxygen, and these chains attain the character of a random coil in very high molecular weight range (degree of polymerization greater than 2000). The large differences in the unperturbed dimensions of cellulosic chains observed in different solvents have been attributed to the possible small changes in the angle τ caused by specific solvent, interactions.
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    Effect of side-chain hydrophobic bonding on the stability of homopolyamino acid α-helices: Conformational studies of poly-L-leucine in waterPresented before the Division of Biological Chemistry at the 154th National Meeting of the American Chemical Society, Chicago, Illinois, September 1967. (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 749-764 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The conformational properties of block copolymers of poly-L-leucine in water have been examined. The degree of polymerization of the poly-L-leucine block was 11 and 21, respectively, for samples prepared by the Merrifield procedure, and 56 for a sample prepared by the polymerization of leucine N-carboxyanhydride. The optical rotatory dispersion parameter b0 was used to obtain the helix content θh at various temperatures. Application of the Lifson-Roig theory gave the following parameters for the transition of a residue from a coil to a helical state: v = 0.05-0.011, ΔH = +100 cal/mole, ΔS = +0.70-1.00 e. u. These parameters, as well as those for other polyamino acids, are accounted for by hydrophobic bonds involving the nonpolar side chains in the helical and randomly coiled forms. From the data for poly-L-alanine and theoretical values of the thermodynamic parameters for hydrophobic bond formation, the parameters for formation of a polyglycine helix are computed. By separating the contributions of the backbone, it is possible to obtain a set of thermodynamic parameters for the side-chain contributions of a number of polyamino acids. Increased size of the nonpolar side chain (with a larger contribution from hydrophobic bonding) makes a larger contribution to the stability of the α-helix which is reflected, among other ways, in a higher helix content at given temperature.
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    Polymerization of amino acid derivatives by polymer catalysts. V. Polymerization of DL-β-phenylalanine N-carboxyanhydride by several poly(N-alkylamino acid) diethylamides (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 791-797 
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    Notes: The polymerization of DL-β-phenylalanine N-carboxyanhydride (NCA) initiated by poly(N-benzylglycine)diethylamide (DEA) and poly(N-methyl-DL-alanine)DEA has been investigated. As previously reported, polysarcosine DEA, poly-N-ethylglycine DEA, and poly-N-n-propylglycine DEA showed marked accelerations in the polymerization of DL-β-phenylalanine NCA as compared with the polymerization initiated by low molecular weight, amines having similar base strength. However, this phenomenon (the chain effect) was not observed with the two polymer catalysts studied in the present investigation With poly-N-methyl-DL-alanine DEA, adsorption of DL-β-phenylalanine NCA onto the polymer chain takes place, though not so effectively as with other polypeptides, so the absence of chain effect was ascribed to a reduced flexibility of the polymer chain. With poly(N-benzylglycine)DEA, the reactivity of terminal base group was found to be much lower than that of other polymer catalysts. However, the absence of the chain effect would be attributed to the rigidity of polymer chain of poly-N-benzylglycine DEA due to the bulkiness of the N-benzyl group.
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    Ionic polysaccharides. III. Dilute solution properties of hyaluronic acid fractions (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 799-810 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: Molecular weights by osmometry (M̄n), light scattering (M̄w), and sedimentation-diffusion (MsD) were determined for selected fractions and unfractionated samples of hyaluronic acid in the molecular weight range 3 × 104-1.7 × 106. For the determination of MsD from the sedimentation coefficient s, a calibration procedure based on the data of Laurent, Ryan, and Pietruszkiewicz gave the following relations in 0.2M NaCl: log (s-1)0 = 14.681 - 0.413 log MsD and log D0 = -3.828 - 0.568 log MsD, where subscript, zero refers to zero concentration and D is the diffusion coefficient. The average Mandelkern-Flory parameter β in 0.2M NaCl is 3.0 × 106. Data for the intrinsic viscosity [η] may be fitted for M 〉 105 by [η] = K′Ma, where K′, a are in 0.2M NaCl, 0.0228, 0.816; in 0.5M NaCl, 0.0318, 0.777; in 0.1 M HCl, 0.0279, 0.763, respectively. Below M = 105, [η] appears to fall below the values calculated, possibly due to non-Gaussian behavior of short chains. The second virial coefficient A2 in 0.5M NaCl approaches the ideal Donnan value, decreasing slightly with increasing molecular weight. The friction parameter P is about 20% smaller than that of uncharged polymers of similar dimensions. The flexible coiling nature of this polymer is confirmed.
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    Sedimentation of ribosomal ribonucleic acid from ribonuclease treated and untreated ribosomes (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 843-864 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The formation of a slowly sedimenting form of 23-S ribosomal RNA from E. coli has been investigated by analytical ultracentrifugation and thermal denaturation in aqueous solution and in formamide. Evidence is presented that the slow form of 23-S arises as a result of nucleate damage to the RNA in the 50-S ribosome. The 30-S ribosome (and 16-S RNA), is unaffected. The slow form of 23-S RNA cannot be demonstrated under conditions of complete denaturation in formamide, but only by partial denaturation in aqueous solution of low ionic strength (〈 0.01M Na). Apparent maintenance of the integrity of 23-S RNA in formamide after nuclease treatment suggests that this may not be a simple linear molecule. An alternative model is suggested containing a circular element in the structure.
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    Mechanochemical study of wet-spun lithium-DNA fibers (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 825-842 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Uniform LiDNA fiber specimens of nearly 20 m length have been prepared with a wet-spinning method developed by the author. Samples immersed in the spinning bath (80% ethyl alcohol containing 0.4M LiCl) have been subjected to mechanochemical study involving stretching, relaxation, and contraction measurements. A special technique was developed to transfer the sample from the Teflon-coated cylinder used in spinning to the sample column of the mechanochemical apparatus without stretching or removing the sample from the spinning bath. Force-strain curves of samples consisting of two fiber bundles showed an initial region of low slope followed by a region of high slope and a second region of low slope up to rupture. Some thicker specimens showed an aging effect which abolished the initial low-slope region and was interpreted as indicative of crystallization. Force-strain curves of two-bundle samples showed a strong influence of temperature with a complete loss of tensile strength of the LiDNA fibers in the spinning bath at about 55°C. Furthermore, samples at zero strain exhibited a contractile force when subjected to temperatures above about 40°C; the contractile process was pronounced with samples kept above 48°C. On contraction these samples obtained a zero-force length 20-30% of the original. These data are taken as evidence for a helix-to-coil transition occurring in the DNA, the low melting temperature being caused by the chemical influence of the ambient aqueous alcohol-LiCl bath.
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    Low-angle light-scattering studies on alkali- and heat-denatured DNA (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1029-1038 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molecular weight of native DNA is shown to decrease by at least a factor of two on denaturation by heat or alkali. This result is obtained only if low-angle (〈30°) light-scattering measurements are used. High-angle measurements (〉30°) do not reveal a decrease in molecular weight on denaturation due to the incorrect value for native DNA. The dn/dc value for both native and denatured DNA is 0.166 ml/g ± 0.003 ml/g. Methods are described for the clarification of native and denatured DNA solutions for light scattering by the use of membrane filters.
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    Electric dichroism studies: Interaction of trifluoroacetic acid with poly(gamma;-benzyl L-glutamate) (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 991-1000 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: Electric dichroism studies on poly(γ-benxyl L-glutamate) show that the addition of small amounts (up to 5%) of trifluoroacetic acid causes complete disappearance of dichroism in contrast to the electric birefringence, which drops to an observable plateau at 20% of its initial value. This loss of dichroism cannot be explained simply by a decrease in the effective dipole moment of the benzyl ester side chains, and the nature of this interaction is explored by nuclear magnetic resonance and infrared spectral studies. Theories of the helix-coil transition which require an initial protonation of the helix backbone to form a more flexible rod consisting of helical segments interrupted by regions of random coil are shown to be inadequate to describe the changes in poly(γ-benzyl L-glutamate) effected by small amounts of trifluoroacetic acid. Rather, trifluoroacetic acid in small amounts interacts with the ester carbonyl oxygen in the side chain, either by hydrogen bonding or protonation, before there is evidence of any effect on the backbone or of loss of helix content.
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    Raman spectra of poly-L-lysines (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1229-1237 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The Raman spectra of poly-L-lysine hydrochloride and poly-∊-carbobenzoxy-L-lysine in the solid state have been obtained and are consistent with the presence of an α-helical structure. The Raman spectrum of poly-L-lysine in aqueous solution suggests the presence of random coil structures.
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    Backbone and side-chain conformations of amino acids and amino acid residues in peptidesContribution No. 288 from the Centre of Advanced Study in Biophysics, University of Madras, Guindu Campus, Madras-25, India. (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1249-1252 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Masthead (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    URL: http://dx.doi.org/10.1002/bip.1970.360091101
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    Conformational studies of linear β-D-1,4′-mannan and galactanContribution No. 289 from the Centre of Advanced Study in Physics, University of Madras, Madras, India. (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1239-1247 
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    Notes: The nonbonded interaction energy of disaccharides, mannobiose and galactobiose and polysaccharides mannan and galactan have been computed as a function of dihedral angles (φ,ψ). The conformation (40°, -20°) has been preferred for the mannan chain from nonbonded interaction energy considerations. The O5…O3′ type of intramolecular hydrogen bond has been found to be possible in the above conformation. Comparison of the allowed region of mannan with those of cellulose and xylan indicates that the monomer unit, in mannan chain has slightly higher freedom of rotation than that of cellulose and less than that of xylan. As in cellulose and mannan, the freedom of rotation of the monomer units in β-1,4′ galactan is highly restricted. Unlike mannan (which prefers an extended conformation) the β-1,4′ galactan prefers a helical conformation similar to amylose. Just as in amylose the O2…O3′ type hydrogen bond between contiguous residues is also possible in β-1,4′ galactan.
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    Perspectives report: Melting of DNA: Its study and application as a research methodWe are delighted to include this article in Biopolymers since it includes the important Russian literature in this area. The Editors. (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1253-1306 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 23 Ill.
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    Critical comparison of the experimental optical activity of helical polypeptides and the predictions of the molecular exciton model (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1475-1502 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The predictions of the presently accepted molecular exciton model for the optical activity of helical polypeptides are in reasonable agreement with experimental spectra in the accessible wavelength range. However, crucial verification requires the detect of a significant negative rotatory hand just below the accessible range. A computer-oriented method is utilized to obtain information concerning the inaccessible range. Optical rotatory dispersion computed by evaluation of the Kronig-Kramers integral transform from the experimentally determined circular dichroism of several helical homopolypeptides in solution are compared with the experimentally determined optical rotatory dispersion. Computed and experimental curves are congruent within an uncertainty approaching that of the experimental technique, whatever the polypeptide sample lot, side chains, and solvent. It is shown that t his agreement is not a computational or experimental artifact. These results can be interpreted in two ways: (1) that the predicted band does not exist, and (2) that the perturbation of the predicted band is being negated by other inaccessible bands in the vacuum ultraviolet. Arguments are presented to show that the first of these two possibilities is more probable.
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    Electrophoretic charge of a cylindrical macroion in aqueous 1 : 1 electrolyte (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1511-1530 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The potential problem is formulated for rodlike macroions and reduced to a single dimensionless equation with appropriate boundary conditions. A method of solution based on piecewise linearization of the potential equation is detailed and compared with two other approaches. It is suggested that the present method yields improved estimates of macroion charges. Some numerical results are included, and the relation between electrophoretic charge and macroion charge is considered.
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    Preface (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. xi 
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    URL: http://dx.doi.org/10.1002/bip.360220103
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    Interactions between poly(Gly-Pro-Pro) triple helices: A model for molecular packing in collagen (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 33-36 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: Potential-energy calculations are reported on the interaction between two collagenlike triple-stranded poly(Gly-L-Pro-L-Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.
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    Coupling between the helix-coil transition and nematic-isotropic transitions in polypeptide solutions (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 43-47 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The lattice model of Flory has been extended in order to consider equilibrium between isotropic and nematic phases containing helix-coil type chains. Nearly complete exclusion of coil sequences from the lyotropic nematic phase produces an enhanced cooperativity in the helix-coil transition. In poor solvents this enhancement begins to occur at concentrations typical of some experiments.
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    Strategy for trapping intermediates in the folding of ribonuclease and for using 1H-NMR to determine their structures (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 59-67 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The major unfolded form of ribonuclease A is known to show well-populated structural intermediates transiently during folding at 0°-10°C. We describe here how the exchange reaction between D2O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by 1H-nmr after folding is complete. The feasibility of using 1H-nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D2O in which only the peptide protons of residues 7-14 are in the 1H-form. All eight of these protected peptide protons are H-bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the 1H-form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H-bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3-13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α-helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.
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    Multiphasic conformation transition of globular proteins under denaturating perturbation (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 93-99 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Denaturation profiles of 17 globular proteins were studied by the spectroscopic and chromatographic methods with high-data-point density. The denaturational transitions are broadly classified into three types according to their multiphasic characteristics. In general, more or less complex internal cooperative events seem to take place in the conformation transition of globular proteins.
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    Conformational and functional properties of hemoglobin in water-organic cosolvent mixtures: Effect of ethylene glycol and glycerol on oxygen affinity (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 119-123 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: We report on the effects that the presence of ethylene glycol or glycerol has on the oxygen affinity of hemoglobin. We attribute these effects to an altered equilibrium between T and R quaternary conformations of hemoglobin and separate them into bulk-electrostatic and non-bulk-electrostatic contributions to the standard free-energy difference between the R and T states.
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    NMR analysis of structure and function of snake neurotoxins (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 139-145 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The 270-MHz proton-nmr spectra of short neurotoxins (erabutoxins from Laticauda semifasciata and cobrotoxin from Naja naja atra) and long neurotoxins (toxin B from Naja naja and α-bungarotoxin from Bungarus multicinctus) have been analyzed. The conformation of erabutoxin b in solution is largely consistent with the x-ray crystal analysis, although the environment of His-7 in solution is definitely different from that in the crystal. The pH-dependent transition has been found for toxin B, indicating that the conformation in neutral solution is different from that in the crystal as grown from acidic solution. The deuterium-exchange rates of the amide protons for the four neurotoxins have been measured. The order of structural rigidity is the same as the order of the irreversibility of neuromuscular block by neurotoxins.
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    1H-NMR studies on poly(oxyethylene)-bound oligopeptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 163-169 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Conformational studies on poly(oxyethylene)-bound homo-, oligo-, guest-host, and sequential peptides synthesized according to the liquid-phase method were carried out by means of 1H-nmr spectroscopy. The solubilizing effect of the C-terminal polymeric support allowed a thorough investigation of the secondary structure in solution.
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    Vibrational analysis of conformation in peptides, polypeptides, and proteinsThis is paper number 16 in a series of which Ref. 20 is paper 15. (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 217-225 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A vibrational force field for the polypeptide chain has been developed for normal-mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm-1. We review the application of this technique to conformational problems in peptides (β-turns and their model compounds), polypeptides [the αII-helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).
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    1H-NMR studies on substance P hexapeptide analogs (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 247-253 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: 1H-nmr studies of [pGlu6]SP6-11, [gpGlu6,mPhe7]SP6-11, and [pGlu6,N-CH3Phe7]SP6-11 in DMSO-d6 reveal characteristic chemical shifts, 3JNH-αCH, temperature dependence, as well as deuterium exchange half-times. Marked similarities are revealed for the two first analogs, whereas the N-methylated analog is clearly different. Possible conformations are considered.
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    Conformational flexibility in a small globular hormone: X-ray analysis of avian pancreatic polypeptide at 0.98-Å resolution (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 293-304 
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    Notes: The 36-amino acid avian pancreatic polypeptide has been studied by x-ray analysis at 0.98-Å resolution and refined using a restrained least-squares technique to an agreement factor of 15.6%. The polypeptide, which has a compact globular structure with a hydrophobic core, comprises a polyproline-like helix (residues 2-8) and an α-helix (residues 14-32). The molecule forms symmetrical dimers linked through zinc atoms in the crystal lattice. The high-resolution analysis defines sequence-dependent distortions in the α-helical parameters due to hydrogen bonding of water molecules and side chains. The thermal parameters indicate an increased flexibility of the main chain at the turn between the helices and in the C-terminal residues. For the first time, six-parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. The physiological roles of conformation, flexibility, and dynamics of this polypeptide hormone are discussed.
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    Solid-state geometry and conformation of linear, diastereoisomeric oligoprolinesAbbreviations, description of the atoms, and conventions for the conformation of the peptide chain follow the recommendations of the IUPAC-IUB Commission on Biochemical Nomenclature [(1972) Biochem. J. 126, 773-780]. Further abbreviations used are: Ac, acetyl; n-Prp, n-propionyl; Mmp, 1-(3-mercapto-2-methylpropionyl); Piv, pivaloyl; t-Boc, tert-butyloxycarbonyl; t-Aoc, tert-amyloxycarbonyl; Z, benzyloxycarbonyl; Hyp, 4-hydroxyproline; Aze, azetidine-4-carboxylic acid; Thz, thiazolidine-4-carboxylic acid; Δβ-Pro, 3,4-dehydroproline; Aib, α-aminoisobutyric acid; Pip, pipecolic acid; pGlu, pyroglutamic acid; OMe, methoxy; OBzl, benzyloxy. (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 305-317 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: We have carried out a systematic analysis of the solid-state conformational preferences of a number of linear homo-oligoprolines (to the tetramer) by ir absorption and x-ray diffraction. The peptides present different chiral sequences (tacticities), various types (urethane and amide) of N-protecting groups, and free and blocked C-termini (which imply different capabilities of forming H-bonds). The following conclusions can be drawn: (i) values for the geometry of the prolyl residue and the peptide bond in the cis and in the trans conformations are proposed; (ii) in general the conformational angles ϕ and ψ in the linear homo-oligoprolines have values appropriate for the polyproline II structure (conformation F); (iii) the pyrrolidine ring shows various types of puckering with no apparent relation to the backbone conformation; (iv) Pro-Pro peptide bonds generally take the trans conformation, the few cases of cis conformation being formed by Pro residues of different chirality; (v) the single H-bond donor  -  OH, when present, is always bonded to H-acceptors, which can be either the urethane or the amide or the peptide carbonyl but never the carbonyl group of the  -  COOH moiety.
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    Microheterogeneity of bovine myelin basic protein studied by nuclear magnetic resonance spectroscopy (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 377-380 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: Myelin basic protein isolated from bovine white matter is known to consist of a mixture of three or more “charge isomers”, which can be separated by cation-exchange chromatography. We are using 360-MHz 1H-nmr spectroscopy to establish the chemical and structural differences among them. Preliminary studies by difference spectroscopy between two of the isomers suggest (a) all aromatic residues, and probably their nearest-neighbors, are unchanged; (b) the less cationic isomer lacks one (or two) of its C-terminal Arg residues; and (c) a significant fraction of the two Met residues in the less cationic isomer is present as methionine sulfoxide.
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    Spectroscopic studies of a hydrophobic peptide in membranelike environments (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 381-385 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A hydrophobic linear peptide has been synthesized and studied over a range of environments using several complementary spectroscopic approaches, including nmr, CD, and vibrational spectroscopies. The sequence of this model peptide, carbobenzoxy-L-Pro-D-Phe-D-Ala-L-Pro-NHCH3, was designed such that a small number of “folded” conformations, stabilized by intramolecular hydrogen bonding, would be accessible to it. Additionally, the extremely hydrophobic character of the peptide favors its interactions with hydrophobic regions of a membrane. The conformational impact of the membrane environment on the peptide, and the effect of the peptide on lipid organization have been explored both in micellar media and in vesicles. To facilitate nmr analysis, the peptide has been synthesized with one of the prolines perdeuterated. Results of these studies reveal that the peptide experiences a microenvironment of moderate polarity in micellar media and causes changes in lipid structure in a vesicle that are indicative of a hydrophobic peptide-lipid interaction.
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    How antigenic are antigenic peptides? (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 425-440 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Most of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody-combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid-phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross-reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72-89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25-55) is also antigenic.
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    Some novel approaches to the design and synthesis of peptide-catecholamine conjugates (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 531-545 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of novel, functionalized catecholamines (congeners) has been synthesized in which, formalistically, the N-isopropyl group of isoproterenol has been extended by a linear alkyl chain of varying length, terminated by a carboxyl group. Model amide derivatives have also been prepared in order to optimize the biological activity of these derivatives and also to aid in the design of appropriate peptides for the synthesis of conjugates. As a result of these studies, a series of amino acid and monodisperse peptide carriers, containing p-aminophenylalanine as the point of attachment for the drug, was prepared, together with the corresponding conjugates. In vitro and in vivo evaluation of the congeners, model amides, and conjugates has demonstrated that the biological activity of these derivatives is extremely sensitive to structural modifications at a point far-removed from the pharmacophore, in both the congener amide and conjugate series. A number of the model amides and conjugates have proven to be highly active when tested in both in vitro and in vivo test systems. The implications of these results in terms of a novel structure-activity approach to drug design are discussed.
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    URL: http://dx.doi.org/10.1002/bip.360220166
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    Specific and nonspecific macromolecule-drug conjugates for the improvement of cancer chemotherapy (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 557-567 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Antineoplastic drugs such as daunomycin, adriamycin, methotrexate, 5-fluorouridine, cytosine arabinoside, and platinate were bound to antibodies directly or via a polymeric bridge. The drug antibody conjugates retained most of their drug and antibody activities when tested in vitro. Daunomycin-antibody conjugates were shown to penetrate tumor cells in the conjugated form. In animals, daunomycin-antibody conjugates were at least as effective chemotherapeutically as the corresponding free drugs and considerably less toxic. In some tumor systems, the daunomycin-antibody conjugates represented an improvement over the free drug. This improvement was restricted in some tumors to a particular injection route of the tumor and the treatment.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220168
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    Synthesis and spectroscopic characterization of insulin derivatives containing one or two poly(ethylene oxide) chains at specific positions (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 569-573 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a synthetic method aimed at specifically coupling poly(ethylene oxide) (PEO) to proteins without altering their spectroscopic properties. To do so, we have first modified the alcohol end group of PEO to an acid end group (PEO-COOH). Coupling of PEO-COOH to Gly A1 methylsulfonylethyloxycarbonyl (Msc) protected insulin yielded NαB1,N∊B29-(PEO)2-insulin. Conversely, coupling of PEO-COOH to insulin whose Gly A1 and Lys B29 amino groups were protected with Msc yielded NαB1-PEO-insulin. The products were obtained in a spectroscopically pure form and characterized by uv and CD spectroscopy. Conformational and biological studies are in progress.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220169
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    Poly(2-aminodeoxyadenylic acid): Circular dichroism and thermal stability of its complexes and their relevance to phage DNA in which A is replaced by 2NH2A (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 597-600 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220204
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    Crystal structure and conformation of a cyclic tetrapeptide cyclo(L-Pro-Sar)2 containing all-cis peptide units (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 633-641 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure and conformation of the synthetic cyclic tetrapeptide, cyclo(L-Pro-Sar)2, was determined by x-ray analysis. The peptide crystallizes in the orthorhombic space group P212121 with cell parameters a = 9.277(1), b = 12.884(1), and c = 15.581(2) Å. The crystal structure was solved by the symbolic addition procedure for direct phase determination and least-squares refinement using 1796 reflections, which led to the final R value of 0.043. This structure provides the first example observed in a crystal of a cyclic tetrapeptide in which all four peptide units have been found in the cis conformation with ω angles deviating slightly by 2°-10° from the ideal value of 0°. It was also found that the two Pro Cα-CO single bonds assumed a trans′ (ψ = 159.6° and 158.4°) conformation. Adjoining average planes of the peptide groups fall at nearly right angles to each other. The pyrrolidine ring conformations of the two prolyl residues are in the envelope form, with Cγ carbon out of the least-squares planes for the remaining four atoms.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220208
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    An analysis of the sequence dependence of the structure and energy of A- and B-DNA models using molecular mechannics (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 969-1002 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A- and B-DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B-DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A-DNA conformation. The molecular interactions responsible for these differential stabilities include both inter- and intrastrand base stacking, as well as base-phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine-3′,5′-pyrimidine sequence over the pyrimidine-3′,5′-purine sequence in both the A- and B-conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate-base and base-base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine-attched sugars and only in the B-DNA geometry. We suggest a molecular mechanism, specifically, differential base-sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220316
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    Salt- and sequence-dependence of the secondary structure of DNA in Solution by 31P-nmr spectroscopy (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 879-893 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We examined three sonicated, specific-seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P-nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P-nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche--gauche- conformation and shifts upfield in all four monovalent salts used, relative to a single-stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans-gauche- conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly-(dAdT) from a presumed right-handed dinucleotide-repeat B-form to another conformation with a dinucleotide-repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans-gauche- conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly-(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right-handed regular B-form to a left-handed Z-form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B-form with a gauche--gauche- phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220310
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    1H-nmr studies on the dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurinenucleosides: Effects of 2′-substitutes on conformation (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1189-1202 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Seven dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurine nucleoside residue, dAfl-U, dAcl-U, dAbr-U, dAio-U, dGfl-U, and dIfl-C, were chemically synthesized and investigated by 1H-nmr spectroscopy at 300 MHz. The sugar and backbone conformations of these compounds were analyzed by the spectral pattern of furanose proton resonances; and the extents of base-base interaction were estimated from chemical shifts and their temperature-dependent changes of base-proton resonances. It is found that the population of C3′-endo conformer and the extent of base-base interaction decrease as the electronegativity of 2′-substituent decreases in dAx-U (x = fl, cl, br, and io) series. The C3′-endo (3E) population and the base-base interaction in Nfl-U (N = A,G)-type dimers as well as dIfl-C are relatively higher than the corresponding natural ribo-dimers but can be recognized as grossly similar to the conformation of regular RNA dimers.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220412
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220501
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