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  • Chemistry  (12,709)
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  • 1965-1969  (6,131)
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  • 1969  (6,131)
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  • 1
    ISSN: 1432-0827
    Keywords: Bacterial amphophile ; Purification ; Chemistry ; Resorption ; Ca influx ; Cyclic AMP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Summary The bone resorptive factor and amphipathic antigen (AcA) previously identified by us in preparations fromActinomyces viscosus have been partially purified, characterized chemically, and compared. They elute at the same location on chromatography with Ac 22. The fatty acid composition of AcA and the bone resorptive factor is the same. Some differences in carbohydrate composition are observed. TheActinomyces factor does not affect calcium influx or cyclic AMP in isolated bone cells. Therefore it is concluded that AcA stimulates resorption either by gaining entrance into bone cells or by way of a yet undetermined second messenger.
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  • 2
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    New York : Wiley-Blackwell
    Biopolymers 8 (1969) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 3
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    New York : Wiley-Blackwell
    Biopolymers 8 (1969), S. 21-27 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An increase in temperature causes an increase in the amplitudes of intramolecular and intermolecular motions and mainfests itself as an increase in the effective radii of the various atoms, especially hydrogen atoms. If one uses a Lennard-Jones 6-12 potential function to account for nonbonded interactions, this increase in the radius of the hydrogen atom is equivalent to a modification of the coefficient of the repulsive part of the Lennard-Jones potential. Accordingly, this effect of increasing temperature on the helix sense of several polyamino acids is computed by allowing the effective radius of the hydrogen atom to increase. It is found that the preferred sense of several polyamino acid helices changes from right- to left-handed as the temperature is increased. This accounts for recent experimental observations of changes in helix sense with temperature.
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  • 4
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    New York : Wiley-Blackwell
    Biopolymers 8 (1969), S. 57-68 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Potentiometric titrations and some complementary optical rotation data are presented for solutions of poly(L- glutamic acid) (PGA) in several H2O-ethanol mixtures. The data allow the determination of the intrinsic pK (pK0), slope of the apparent. pK (pKapp), versus degree of ionization curves and of the enthalpy of ionization as a function of ethanol concentration. The variation of the degree of ionization at which the helix-coil transformation occurs with ethanol and temperature is also determined. Finally free energy, enthalpy, and intropy changes associated with the helix-coil transformation for the uncharged conformers are determined from the titration curves. The effect of the ethanol is to increase the stability of the helical conformation of PGA for both the charged and the uncharged forms of the polymer. The stabilization of the uncharged helix is essentially an entropic effect.
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  • 5
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    Biopolymers 8 (1969), S. 91-99 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Infrared spectra of polypeptides were measured in the region of 1800-400 cm-1. For the α-helical form, disordered form, and antiparallel-chain β-form, amide V band- arising from N-H out-of-plane bending models were observed at 610-620, around 650, and 700-705 cm-1, respectively, and amide V′ bands arising from N-D out-of-plane bending modes were observed at 455-465, around 510, and a 515-530 cm-1, respectively. These correlations are useful for conformation diagnoses, particularly for copolyamino-acids or proteins which are not oriented. The nature of low-frequency amide bands are discussed with reference to potential energy distributions calculated for the α-helical form and β form.
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Some experimental data are given on the infrared spectra between 3300 and 3500 cm-1 of dilute solutions in carbon tetrachloride of three types of model compounds: CH3-CONH-CH(R1)-CONH(R2), (I); CH3-CON(CH3)-CH(R1)-CONH(R2), (II) and CH3-CONH-CH(R1)-CON(R2)2, (III). In studying the N-H stretching bands, it was found that there are two types of intramolecular hydrogen bonds in these molecules; these result in two different cyclized conformations, C5 and C7, which contain respectively, five and seven atoms in the ring. By using model substances I, II, and III, in which the nitrogen atoms are unequally substituted, it is possible to identify the N-H stretching bands which are to be ascribed to the N-H oscillators included in the two different chelated conformations. It is found also that the stretching frequency of a free N-H oscillator depends upon the substituent on the nitrogen atom. Thus, it is possible to observe, with some of the model compounds I, four different absorption bands located at 3340, 3420, 3440, and 3460 cm-1. The first two are ascribed to the N-H oscillators included in the H—bonds which lock the C7 and C5 conformations; the last two correspond to free N-H which differ with the substituent on the nitrogen atom.
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  • 7
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    Biopolymers 8 (1969), S. 153-155 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 8
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    Biopolymers 7 (1969), S. 207-213 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular orbital calculations of the extended Hückel type have been used to study the conformations of glycyl and alanyl residues in ground and excited states. The ground-state surfaces show features similar to those obtained with the standard calculational methods in which the total energy is partitioned into components such as torsions, nonbonded and electrostatic interactions. The molecular orbital calculations provide the first independent theoretical check on such calculations. The excited-state surfaces, Uniquely available from the molecular orbital calculations, exhibit a better definition and sharpening of potential minima in the sterically allowed regions.
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  • 9
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We derive equations for calculating the number-, weight-, and z-average lengths between single-strand breaks in DNA molecules. Provision is made for the existence of preformed breaks under genetic control: these are assumed to be fixed in number in each molecule, but may be variable in position. Breaks due to random degradation may be superimposed on the pre-existing breaks. An example is given for illustrative purposes.
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  • 10
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    Biopolymers 7 (1969), S. 223-239 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation in solution of fractionated 30 S and 19 S ribosomal RNA from rabbit reticulocytes has been studied by optical rotatory dispersion, analysis of thermal melting profiles and their derivatives, and spectrophotometric acid-base titration. From a consideration of the limitations of these methods, it has been possible to set limiting values on the degree of base-pairing and the lengths of the double helices: between 60 and 80% of the bases in 19 S and 30 S RNA are estimated to be paired. The paired segments are not shorter than 4 base pairs, and evidence from other sources is available which indicates that they are not longer than 8-16 base pairs. The spread of helix lengths is greater in the 30 S than in 19 S RNA; and other differences are noted. Several distinct populations of double helices, differing in their thermal stability, are present. Estimates are presented from spectrophotometric and titration data for the base compositions of the paired and unpaired regions.
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  • 11
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    Biopolymers 7 (1969), S. 251-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A small perturbation analysis is carried out to determine the stability of a fluid containing two layers of diffusing solutes in a common solvent and acted upon by a uniform gravitational field. It is found that instability can arise even though the unperturbed diffusion does not lead to the formation of a density inversion within the fluid.
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  • 12
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 13
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    Biopolymers 7 (1969), S. 475-493 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of denaturation of DNA have been studied by relaxation techniques. Examination of the terminal relaxation times for a variety of DNA's under a variety of conditions has shown that DNA denaturation is principally a hydrodynamically limited process. Measurements within the helix-coil transition have demonstrated that the experimentally measured terminal relaxation times are a function of the following: (1) position in the helix-coil transition; (2) ionic strength of the solvent; (3) solvent viscosity; (4) DNA concentration; (5) molecular weight; (6) number and position of single-strand breaks. The dependence of the terminal relaxation time on the above mentioned factors can be attributed to hydrodynamic effects. Thus a hydrodynamic model for DNA unwinding is required. The model which best fits the data involves the assumption of a rotational frictional coefficient independent of molecular weight. This assumption is suggested by the fact that the relaxation time is proportional to the first power of the molecular weight.
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  • 14
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    Biopolymers 7 (1969), S. 495-502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Sodium counterion association with partially neutralized poly(D-glutamic acid) or poly(DL-glutamic acid) was measured by use of Wall's transference method with radioactive sodium. In the region where both polyacids are in completely random coil form, fractions of association were considerably less than that with poly(acrylic acid) in the same region of degree of neutralization. Even in the region where poly (D-glutamic acid) is in the helical form, the fraction of association was less than that with poly(acrylic acid) in the same region. No pronounced characteristics attributable to counterion association corresponding to the helix-coil transition could be found. The association phenomena were discussed on the basis of a rodlike model of polyelectrolyte.
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  • 15
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    Biopolymers 7 (1969), S. 411-415 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The isomerization of poly-L-proline in different solvents has been studied by NMR spectroscopy. Different resonance signals for the CHα protons have been obtained for the two different helical conformations of thus compound, namely form I and form II.
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  • 16
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    Biopolymers 7 (1969), S. 417-422 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly-β-N-diphenylmethyl-L-asparagine and poly-γ-N-diphenylmethyl-L-glutamine were prepared from the corresponding N-carboxyanhydrides. Poly-L-aspuragine and poly-L-glutamine were obtained by removal of the diphenylmethyl protecting groups with liquid anhydrous hydrofluoric acid.
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  • 17
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    Biopolymers 7 (1969), S. 379-393 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Hydrogen-tritium exchange character of poly-D,L-alanine was studied in detail as a model for the hydrogen exchange behavior of the unhindered, polymeric peptide group. The random chain nature of poly-D,L-alanine was evident in the uniformity of exchange rate of all its hydrogens and in the similarity between this rate and that of random chain poly-D,L-lysine and other known, unhindered secondary amide groups. An equilibrium isotope effect favoring the binding of tritium over protium to the extent of 21% was measured. Specific acid and base catalysis of the exchange and the absence of detectable general catalysis were demonstrated. Apparent energy of activation is 17 kcal/mole for deprotonation, largely due to dependence of Kw on temperature, and 15 kcal/mole for protonation, which correlates with the extreme apparent pK. The hydrogen -tritium exchange half-time rate; of poly-D,L-alamine at any pH and temperature (T: °C) is given by the equation: \documentclass{article}\pagestyle{empty}\begin{document}$$ \[t_{\frac{1}{2}} \,(\min )\, = \,200\,\, \times \,10^{0.05{\rm T}} /\,[10^{{\rm pH} - 3} \, + \,10^{3 - {\rm pH}} ]\] $$\end{document}
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  • 18
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    Biopolymers 7 (1969), S. 581-593 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The specific rotation of starch components, corrected for refractive index variation, exhibits a discontinuity in the region of the water-dimethyl sulfoxide (H2O-DMSO) system that corresponds to the composition of the complex 2H2O-DMSO. This discontinuity is a property dependent upon the presence of a number of consecutively linked α-1,4 glucose units and, therefore, must reflect a change in symmetry of a segment, of polymer chain. The optical rotation of amylose between 26.5 and 92.5°C. does not change in DMSO and is only slightly lowered in water at the higher temperature. The behavior of amylose in both DMSO and H2O is like that of a random coil, as indicated by viscosity and sedimentation measurements. These results may be interpreted either as being compatible with models of amylose in solution in which the polymer backbone has helical twist, or as indicating removal of strong interactions between polymer chain segments by a good solvent.
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  • 19
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 20
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    Biopolymers 7 (1969), S. 614-618 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 21
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    Biopolymers 21 (1982), S. 17-24 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Computer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two-step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.
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  • 22
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    Biopolymers 21 (1982), S. 79-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aldehydes present in acid-soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin-treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α-chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β-chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
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  • 23
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    Biopolymers 21 (1982), S. 147-157 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe conditions which lead to complete helix formation of poly(I) in the presence of NH4+. Binding of NH4+ is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH4+-poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH4+. A stereospecific model is proposed for the NH4+-poly(I) helix in which the N of NH4+ is located on the axis of the four-stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH4+, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
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  • 24
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    Biopolymers 21 (1982), S. 159-167 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson-Boltzmann theory, is an encapsulating δ-function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson-Boltzmann equation.
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  • 25
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    Biopolymers 21 (1982), S. 203-218 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA-bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron-nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2-3-fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order-of-magnitude increase in their rotational correlation time are attributed to hydrogen-bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
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  • 26
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    Biopolymers 21 (1982), S. 265-275 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dc electrical conductivity of films of the polyelectrolyte complexes of glycol chitosan (GlChi) with the sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) was measured at temperatures above and below room temperature. The maximum field strength in the thinnest film used amounted to 3 × 104 V/cm. A plot of normalized current against the reciprocal of the absolute temperature revealed two regions with different slopes, and activation energies in these two regions have been obtained for all the complexes. The activation energies in the high-temperature region vary from 0.85 to 1.18 eV and in the low-temperature region from 0 to 0.22 eV. Reasons are given to show that the conductivity is probably ionic. Near room temperature, the current-voltage relation is almost linear in the GlChi-DS complex, while in the other three complexes the current varies as a power n of the voltage with the value of n ranging from 1.7 to 2.5. A rise in temperatures causes an increase in the slope of the log I vs log V plot in GlChi-DS and GlChi-CMC complexes. The nonlinear current-voltage relation is ascribed to a space-charge-limited conductivity.
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  • 27
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    Biopolymers 21 (1982), S. 301-319 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Five different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge-shaped crystals) or mannan II (hydrated gel-forming pseudo-fibrillar precipitate). High-molecular-weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low-molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base-plane unit-cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish-kebab structures that were characterized.
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  • 28
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer-water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06-0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption-desorption scanning experiments were performed on a globular protein (α-chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.
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  • 29
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    Biopolymers 21 (1982), S. 451-458 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The light scattering of bovine serum albumin (BSA) has been measured at protein concentration up to 90 g/L and at pH values between 4.4 and 7.6. The dependence of scattering on both protein concentration and pH may be quantitatively accounted for by a simple extension of the hard-sphere model for protein solutions [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol. 112, 437-452] allowing for electrostatic repulsions between molecules. According to the extended model, the radius of the effective hard spherical particle representing BSA varies with the net electrical charge of the BSA molecule in a manner which may be calculated from electrostatic theory.
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    Biopolymers 21 (1982), S. 475-497 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2-Cβ-exo-Cγ-endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.
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  • 31
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    Biopolymers 21 (1982), S. 547-563 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectrum of the enzyme adenylate kinase has been investigated. Theoretical calculations, based on the x-ray crystal structure, have been carried out by means of an origin independent matrix formalism. The entire molecule was included in the calculations in the sense that essentially all electronic transitions that occur at wavelengths longer than 185 nm were included in the basis set. A linear dielectric function was utilized to evaluate the intertransition coupling potentials. The results of the theoretical calculations were in reasonable agreement with experimental CD spectra of the molecule.
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  • 32
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    Biopolymers 21 (1982), S. 633-652 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mode of action of many antitumor agents entails the inhibition of nucleic acid synthesis. Because many of the drugs can intercalate, it is assumed that intercalation is an important step in the mechanism of biological activity. As intercalants contain a planar chromophore as an ingredient essential for intercalation, chromophores that should fit into DNA are desired. This is the main theme of this investigation. Binding to DNA of fundamental moieties, protonated pyridine, aniline, phenol, quinone, and 4H-thiopyran-4-one, is studied to determine their optimum placement in DNA. The optimum orientations for each moiety are superimposed to form polyaromatic systems that can intercalate in a manner in which functional groups on these chromophores are oriented as in the moieties themselves. Ideal intercalants proposed contain three and four fused ring system, have protonated ring nitrogen atoms located to maximize the electrostatic interactions with DNA, hydroxy and amino groups that can hydrogen bond to the OII and O5′ phosphate backbone atoms, and carbonyl and sulfur groups in the central position of the ring system to provide variations in the chromophore and to interact with the relatively positive region in the intercalation site. The optimum orientation occurs when the chromophore and the base pairs overlap to the maximum extent. The ideal intercalants are fundamentally of the type:
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  • 33
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    Biopolymers 21 (1982), S. 665-677 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA reassociation kinetics using the phenol emulsion reassociation technique (PERT) [Kohne, D. E., Levison, S. A. & Byers, M. J. (1977) Biochemistry 16, 5329-5341] has been investigated at high DNA concentrations using an endonuclease S1 assay of reaction progress. Apparent second-order rate constants fall on two intersecting straight lines when presented as a function of DNA concentrations on a log-log plot. In the low DNA concentration range, the rate constants drop about 10-fold when concentration increases 1000-fold. In the high DNA concentration range, the rate constants drop more than 10-fold when concentration increases 10-fold. The slopes of these lines are the same in different solvents and at different temperatures. The intersection between the lines occurs when the available catalytic surface is saturated. At high DNA concentrations, high-complexity heterologous denatured DNA apparently competes 2-4 times better for the surface than homologous DNA because it does not participate in a reassociation reaction. Native and partially native DNA molecules cannot compete with single-stranded DNA for a saturated surface. At high DNA concentrations, reactions using PERT become dependent on the single-strand DNA length. Increasing length lowers reassociation rates.
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  • 34
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 35
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    Biopolymers 21 (1982), S. 859-872 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Classical potential functions (CPF) calculations on 3′-mononucleotides, the building blocks of nucleic acids, predict a correlation between the sugar ring pucker and the torsion angle Φ′ around the C3′—O3′ bond. In ribonucleotides, the value of Φ′ depends on the sugar pucker, viz. the C2′-endo sugar pucker is associated with Φ′ = 210° and 270°, while the C3′-endo sugar pucker favors only Φ′ = 210°. On the other hand, in deoxyribonucleotides, both sugar puckers show a preference for Φ′ = 180°. These theoretical predictions are fully corroborated by the results obtained from x-ray and nmr studies on mono-, di-, and polynucleotides.
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  • 36
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The effect of several surfactants on the secondary structure of bovine β-lactoglobulin B was determined from the circular dichroism spectra. The spectra were measured at several concentrations of surfactant ranging from 1 mg/mL to the critical micelle concentration. The surfactants studied were sodium dodecyl, decyl, and octyl sulfate, sodium dodecyl sarcosinate, dodecyltrimethylammonium bromide. The data were analyzed using the method of Chen et al. [Biochemistry (1974) 13, 3350-3359] to determine the percentage of α-helix, β-sheet, and unordered form at each surfactant concentration. In every case, an increase in structured form and a 20-25% decrease in the amount of unordered form was noted when the surfactant concentration reached the critical micelle concentration. However, the relative amounts of the two structured forms present depend on the surfactant used. The profile of the secondary structure of the protein also varied from surfactant to surfactant as the protein was titrated, probably reflecting the delicate balance between ionic and nonionic forces that governs the secondary structure of β-lactoglobulin and most other globular proteins in aqueous solution.
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  • 37
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amino acids are known to differ in their individual preferences for each of the four positions of the β-turn conformation formed by tetrapeptide segments. Proline and glycine show relatively high preferences for positions 2 and 3, respectively, of the β-turn. Using tripeptides of the type N-acetyl-Pro-Gly-X-OH, where X = Gly, Ala, Leu, Ile, and Phe, we have sought to study the influence of the 4th residue X on the stability of the β-turn conformation in these tripeptides. Our nmr and CD results show that the β-turn stability is quite significantly governed by the nature of the amino acid residue at this position in the following order: Leu 〉 Ala 〉 Ile, Gly 〉 Phe.
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  • 38
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    Biopolymers 21 (1982), S. 1153-1166 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Thermodynamic studies of the binding of adamantanecarboxylate to cyclodextrins have been made as a function of temperature and added organic cosolvent (methanol) using flow microcalorimetry. The negative heat capacity change associated with the adamantanecar-boxylate/β-cyclodextrin interaction and the fact that the interaction is weakened by the addition of methanol implicate the binding process as being a hydrophobically driven one. The negative enthalpy change (ΔH0 = -5.5 kcal/mol) and near-zero entropy change (ΔS0 = 1.5 cal/mol deg) are quite different from the values normally expected for a hydrophobic bond, indicating that other bonding forces are important in addition to the hydrophobic effect. The relative contribution of the hydrophobic effect and other bonding forces (most likely van der Waals forces) to the overall binding was judged from an analysis of the dependence of the thermodynamics of the association process on the surface tension of the water-methanol mixtures following a model for “solvophobic” bonding described by Sinanoglu [Molecular Associations in Biology (1968) Academic Press, New York, pp. 427-445]. From this analysis, adamantane-carboxylate/cyclodextrin complex formation is found to be driven to the extent of -1.9 kcal/mol by the hydrophobic effect. Furthermore, the hydrophobic driving force is found to be characterized by a positive ΔS0 of 10 cal/mol deg. The remaining free energy of binding (and the ΔH0 of binding of ∼-6 kcal/mol) is then due to the intrinsic (surface-tension-independent) van der Waals interaction between the ligand and cyclodextrin cavity.
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    Biopolymers 21 (1982) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 40
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are φPro = -57.8°, ψPro = 139.3°, φAib = 61.4°, and ψAib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.
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  • 41
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    Biopolymers 21 (1982), S. 1333-1363 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The folding-unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only Cα and Cβ atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (φ,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding-unfolding transition for this idealized model is an “all-or-none” type; this is attributable to the specific long-range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding-unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium-range contacts at a β-turn and at the α-helix. (2) These grow to include the native pair of interacting β-strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long-range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.
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  • 42
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.
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  • 43
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    Biopolymers 21 (1982), S. 1469-1472 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 21 (1982), S. 1479-1487 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formalism for extracting the conformations of a proline ring based on the bistable jump model of R. E. London [(1978) J. Am. Chem. Soc. 100, 2678-2685] from 13C spin-lattice relaxation times (T1) is given. The method is such that the relaxation data are only partially used to generate the conformations; these conformations are constrained to satisfy the rest of the relaxation data and to yield acceptable ring geometry. An alternate equation for T1 of 13C nuclei to that of London is given. The formalism is illustrated through an example.
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  • 45
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    Biopolymers 21 (1982), S. 1521-1534 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used broadline proton magnetic resonance to study molecular motion in cellulose, a sodium pectate solution, a calcium pectate gel, and isolated bean cell walls. All samples were prepared in D2O to minimize the contribution of water to the observed signals. For each sample, a free induction decay was obtained, and the second moment, spin-lattice relaxation, and dipolar relaxation were measured. Our results show that the large majority of protons in cellulose are immobile. Rigid and mobile domains were also observed in the pectate samples. We have shown that gelation induces large-scale changes in the free induction decay, the second moment, and the relaxation behavior of the pectate. As with the other samples, rigid and more mobile domains were found in bean cell walls. The fraction in the rigid domains is much larger than the fraction of cellulose in the sample, suggesting that the noncellulosic wall components are also organized into rigid and mobile domains.
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  • 46
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Conformational energy computations were carried out on collagenlike triple-stranded conformations of several poly(tripeptide)s with the general structure CH3CO—(Gly—X—Y)3—NHCH3. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly-X-Pro, Gly-X-Ala, Gly-Pro-Y, and Gly-Ala-Y. Minimum-energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α-aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a —Ch2—CH3 side chain in Abu was mapped as a function of the dihedral angle χ1. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X-Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X-Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple-stranded structure.
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    Biopolymers 21 (1982), S. 1657-1666 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ionization constants of the tyrosyl groups of chymotrypsinogen and of nitrated-chymotrypsinogen (two tyrosyl residues nitrated) have been determined by difference spectrophotometry. In chymotrypsinogen, two of the four tyrosyl groups ionize without any time dependence. Above pH greater than ca. 12.5, time-dependent spectral changes are seen for 0.7 group equivalent. The data can be fitted to the values of pK′1 9.75 ± 0.07, pK′2 11.55 ± 0.05, pK′3 13.30 ± 0.05. In nitrated-chymotrypsinogen, the two nitrated tyrosyl residues have pK′1 6.44 and pK′2 8.30. For both proteins, these pK′ values are in agreement with those evaluated from potentiometric titration and calorimetric data using computer-assisted curve-fitting analysis.
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    Biopolymers 21 (1982), S. 2195-2203 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of several samples of poly(α,β-L-Asp) with a molar fraction of β-bonds ranging from 0.1 to 0.55 was investigated by means of ir and CD spectroscopy and potentiometric titration and compared with the results obtained previously with poly(α-L-Asp). All samples investigated underwent a conformational change induced by changes in their degree of ionization: unpronounced ir absorption of amide V at 650 cm-1 was shifted to 620 cm-1 and substantially increased on deionization; CD spectra changed with the degree of ionization, passing through an isosbestic point; and the pattern of the titration curves was more complex than that of a simple polyelectrolyte. The conformation developing with the decreasing degree of ionization may be considered to be α-helix, as deduced according to the analogous behavior of other polypeptides. The extent of the conformational change in the individual samples depends on the molar fraction of β-bonds: the higher it is, the lower is the helix-forming ability of the sample.
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    Biopolymers 21 (1982), S. 2225-2239 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of 1H-nmr spectroscopy is demonstrated to be a useful analytical method to characterize the structure of synthetic peptides attached to soluble, macromolecular polyoxyethylene (POE) supports in the liquid-phase method (LPM) of peptide synthesis. We report an extensive 360-MHz 1H-nmr study of POE-bound homo-oligo-L-methionine peptides. A combination of high field and selective saturation or Redfield pulse methods allows resolution of individual backbone NH and α-CH resonances of dilute peptides in the presence of strong resonances from macromolecular POE and/or protonated solvents. The nmr spectra for the POE-bound peptides in CDCl3 are qualitatively similar to those of the low-molecular-weight Boc-L-Metn-OMe peptide esters. This corroborates other observations that POE has little effect on peptide stucture. The backbone α-CH region of peptides is overlapped by signals from the terminal oxyethylene group of POE, but the peptide side-chain and low-field backbone NH resonances are well resolved. In trifluoroethanol the Boc-(L-Met)n-NH-POE heptamer and octamer adopt the right-handed α-helical structure, and the present nmr studies provide evidence for two strong intramolecular hydrogen bonds to stabilize the helices. In water, the N-deblocked derivatives, (L-Met)n-NH-POE oligomers adopt β-sheet structure and manifest well-resolved nonequivalent NH resonances with 6-7 Hz 3JNH-CH coupling constants.
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    Biopolymers 21 (1982), S. 2241-2252 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The concerted model of Monod, Wyman, and Changeux is generalized so that all effects of interactions for an enzyme operating at a nonequilibrium stationary state are considered. In contrast to the original model, which is based on an analogy to equilibrium ligand binding, the generalization may show both “positive” and “negative cooperativity” in both catalytic binding and conformational processes. Furthermore, in contrast to any equilibrium binding model, the Hill coefficients may be greater than the number of sites n. For catalysis, the maximum value is 2n, and for conformational changes, n + 1. These points are illustrated by two cases that yield simpler analytic expressions. The first obtains when catalysis occurs on a much faster time scale than the conformational changes, and the second, when this situation is reversed.
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    Biopolymers 21 (1982), S. 2315-2316 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 21 (1982), S. 1473-1477 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 21 (1982) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 21 (1982), S. 1503-1520 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: By combining gel permeation chromatography (GPC) and light-scattering spectroscopy, including photon correlation and angular distribution of absolute scattered intensity, we were able to characterize immunologically active Haemophilus influenzae type b polysaccharide (HIB Ps) bovine serum albumin (BSA) conjugates in terms of equivalent hydrodynamic radius rh ∼ (6.2 ± 0.6) × 102 Å, apparent radius of gyration rg ∼ (5.4 ± 0.3) × 102 Å, apparent molecular weight Mw ∼ (3.5 ± 0.4) × 106 g/mol, and a second virial coefficient A2 ∼ (1.9 ± 0.3) × 10-4 cm3 mol/g2. We could study the effects of each of the processes in the conjugate formation according to the following procedure: BSA (dialysis, modification, fractionation) + HIB Ps → HIB Ps/BSA conjugate (conjugate formation, fractionation). Narrow distributions of HIB Ps BSA conjugate formation can be achieved using fractionated BSA.
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    Biopolymers 21 (1982), S. 1569-1586 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ∼25 to ∼500 cm-1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm-1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm-1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm-1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.
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    Biopolymers 21 (1982), S. 1735-1747 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the oxygen replacement reaction of carbon monoxide-saturated hemoglobin (HbA0) was carried out using spectroscopic, calorimetric, and pH titration methods. Under fully saturated conditions the replacement reaction can be defined by a single partition constant over all ratios of bound oxygen to carbon monoxide. This indicates that under saturating conditions Haldane's first law for the ligand binding of gas mixtures holds for any CO/O2 ratio. It further shows that there is no appreciable difference in relative CO-O2 affinity between the α- and β-chains. The same partition coefficient was found to hold for different pH, buffer, and allosteric effector conditions. The lack of any pH dependence of the partition coefficient was confirmed by the absence of proton changes for the replacement reaction. The temperature dependence of the partition coefficient and calorimetric results yield a value for the enthalpy of the reaction of -3.65 ± 0.29 kcal/mol/heme.
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    Biopolymers 21 (1982), S. 1763-1780 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We demonstrate that the isotropic absorption and linear dichroism in an unknown flow field can be used to determine base tilt in polynucleotides if three transitions are measured and the directions of the corresponding dipoles are known. The method is applied here to reach conclusions about the base tilt in poly(rA), poly(rA)+·poly(rA), and poly(rC). The respective values are: 28° tilt about the axis + 50° toward C8 from the C1′ → N9, and 25° tilt about the axis + 118° toward C5 from C1′ → N1. The results for poly(rA)+·poly(rA) are consistent with the accepted model. Spectra were measured for poly(rC)+·poly(rC), but definite conclusions must await reliable directions for transition dipoles. The dipole direction for the 218-nm transition in rC is found to be +13° or +43° toward C5 from C1′ → N1. The CD spectra to about 168 nm are presented and discussed.
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    Biopolymers 21 (1982), S. 1811-1832 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of stress relaxation in uniaxial extension and associated time-dependent birefringence have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 13-22% fibrin plasticized with either aqueous buffer or glycerol. Both unligated and ligated (i.e., with α-α and γ-γ ligation by fibrinoligase, factor XIIIa) films were studied. Both types showed two stages of stress relaxation, with time scales of approximately 10 and 103-104 s, respectively, with a plateau region between. In the plateau, the nominal (engineering) stress for ligated glycerol-plasticized film is proportional to In λ, where λ is the stretch ratio, up to λ ≅ 2, and it decreases with increasing temperature. For unligated glycerol-plasticized film, the stresses are smaller by a factor of one-half to one-third. For ligated film, the second stage of relaxation is relatively slight, and recovery after release of stress is often nearly complete. For unligated film, the second stage involves a substantial drop in stress, and after recovery there is a significant permanent set. A second relaxation for ligated film reproduces the first, but for unligated film it reproduces the first only if the initial relaxation is terminated before the second stage; otherwise, the second relaxation shows a weaker structure. The behavior of water-plasticized film is similar to that of glycerol-plasticized except that the second stage of relaxation occurs at shorter times. During the first stage of stress relaxation, up to about 100 s, the birefringence and the stress-optical coefficient increase; during the plateau zone of stress relaxation, the birefringence of ligated films is approximately constant and is proportional to 2λ2/(λ2 + 1) - 1, where λ is the stretch ratio. This dependence is predicted by a two-dimensional model in which rodlike elements in the plane of the film are oriented with independent alignment. During the final stage of stress relaxation, the birefringence of ligated films decreases slightly; that of unligated films decreases substantially, but less rapidly than the stress, corresponding to a further increase in the stress-optical coefficient. With additional information from small-angle x-ray scattering reported in an accompanying paper, the first stage of relaxation is attributed to partial release of bending forces in the fibers by orientation, accompanied by increased birefringence. The second stage is attributed, for ligated films, to an internal transition in the fibrin units accompanied by elongation of some of the fibers; and in the unligated films, to a combination of the latter transition with slippage of protofibrils lengthwise within the fiber bundles that causes some loss of orientation, which diminishes the birefringence.
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    Biopolymers 21 (1982), S. 1899-1908 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A microscope capable of measuring the CD of intact single eukaryotic cells, DNA microcrystals, and other microscopic structures has been constructed and tested. It can measure the CD spectra in the 200- and 800-nm wavelength range and consists of a modification to a standard Cary 60 CD machine in combination with a Zeiss uv microspectrometer. Preliminary CD spectra of red blood cells and lymphocytes are presented.
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    Biopolymers 21 (1982), S. 1909-1926 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of fibers in agarose gels has been studied by electron-microscopic examination of replicas formed from freeze-fracture surfaces. For gels set in water, the results obtained support the model proposed for the gel structure by Arnott et al. (1974) of a random array of long, straight, connected fibers, with each fiber having a diameter equivalent to that of an aggregate of approximately 10-30 agarose helixes, depending on the initial agarose concentration. The density of these fibers, their water content, and the total length of fibers per unit volume have been derived from the measured distribution of intersections per unit area of freeze-fracture surfaces. For gels set in the presence of salt, the distribution of fibers becomes distinctly non-Poissonian, leading to larger interfiber spaces and a gel of greater effective pore size. The larger pore size of gels set in the presence of salt also has been revealed by electrophoretic measurements in which the relative migration rates of plasmid DNA molecules of varying conformations have been determined.
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    Biopolymers 21 (1982), S. 1933-1943 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Energy embedding has been shown recently to be a useful extension of the distance geometry approach to conformational calculations in the case of very small molecules and simple energy functions. This paper tests the ability of energy embedding to locate low energy conformations satisfying both weak and strong geometric constraints when the molecule is the small protein, bovine pancreatic trypsin inhibitor, and the energy function is the complicated Oobatake-Crippen residue-residue potential. Using the potential function alone, the algorithm reaches a structure with energy lower than that of the native conformation, but with little resemblance to it. Aided by numerous geometric constraints, such as preformed secondary structure segments, the algorithm again finds a local minimum with energy better than that of the native, and with only 3.3 Å rms deviation from it. This is significantly closer to the native value than can be obtained using standard distance geometry and the geometric constraints alone. Thus, energy embedding using the Oobatake-Crippen potential function is a significant help in finding native conformations of proteins. However, additional trials on a hairpin bend fragment of trypsin inhibitor demonstrate the potential's shortcomings in encouraging proper secondary structure.
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  • 62
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    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 2179-2185].We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche- to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche- to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base-base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.
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    Topics: Chemistry and Pharmacology
    Notes: The microwave absorption of aqueous solutions of DNA extracted from E. coli has been studied between 8 and 12 GHz by the use of an optical heterodyne technique. By measuring optically the temperature rise produced in an absorbing sample by pulsed microwave radiation, unambiguous, direct measurement of the microwave absorption is possible. Our results show that E. coli DNA absorbs microwaves in the 8-12-GHz region substantially more efficiently than water, which is itself an extremely efficient absorber. The observed absorption is featureless and decreases slightly with increasing frequency. These observations are consistent with an explanation involving direct absorption by longitudinal acoustic modes of the double helix.
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    Biopolymers 21 (1982), S. 251-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formation of polyelectrolyte complexes of glycol chitosan (GlChi) with sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) has been studied. The number of ionizable groups per pyranose ring and the degree of dissociation as a function of pH in the polycation and polyanions have been determined using conductometric and potentiometric titrations. The formation of the complexes at different pH values has been followed by turbidity measurements. It is found that stoichiometric complexes of the polycation with CMC, (GalUA)n, and AlgA are formed at a mixing ratio of 0.5, indicating that the conformation may correspond to chains of equal lengths. In the case of the complex of GlChi with DS, the stoichiometric composition corresponds to a mixing ratio of 0.62. Thin transparent films of the complexes have been obtained by dehydration under reduced pressure on a layer of mercury. The dielectric constant ε′ and loss ε″ of thin films of these complexes have been measured in the range of frequencies of 1-100 kHz at different temperatures above and below room temperature. The GlChi-DS complex shows very little change in the values of ε′ and ε″ with frequency or temperature. On the other hand, films of GlChi-CMC and GlChi-(GalUA)n complexes show a significant increase in ε′ and ε″ as the temperature is increased above room temperature. The increase is more prominent at low frequencies. This behavior is attributed to the Maxwell-Wagner interfacial polarization. In the case of GlChi-AlgA film, the values of ε′ and ε″ increase enormously as the temperature increases. This behavior is similar to the increase in ε′ and ε″ observed by Michels et al. [(1965) J. Phys. Chem. 69, 1456-1465] as the salt concentration increases in another polyelectrolyte complex studied by them. The electric double-layer mechanism proposed by Schwarz [(1962) J. Phys. Chem. 66, 2636-2642] to account for the dielectric properties of biocolloids is shown to account quantitatively for the observations on the GlChi-AlgA film.
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    Chemie in unserer Zeit 16 (1982) 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 16 (1982), S. 35-45 
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    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 16 (1982), S. 69-70 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 16 (1982), S. 94-100 
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    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 16 (1982), S. A32 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 16 (1982), S. 116-123 
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    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Chemie in unserer Zeit 16 (1982), S. A46 
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    Chemie in unserer Zeit 16 (1982), S. 149-159 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
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    Topics: Chemistry and Pharmacology
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    Biopolymers 7 (1969) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 7 (1969), S. 1-3 
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    Biopolymers 7 (1969), S. 5-19 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The osmotic pressure equation for nonideal, associating systems of the type nA +mB ⇄ AnBm, has been derived, by using the assumption yAnBm/yAnyBm = 1. This treatment can also be applied to related associations such as nA + mB ⇄ AB + AB2 + A2B + …. From osmotic pressure experiments on the pure reactants it is possible to obtain the molecular weights (MA and MB) of the reactants and also the virial coefficients (BAA and BBB) of the reactants. The osmotic pressure of a nonreacting mixture of A and B can be calculated from these measurements. It can be used along with osmotic pressure measurements on equilibrium mixtures of A and B to obtain expressions containing the equilibrium constant (or constants) and the cross-virial coefficients (BAB and BBA). Several procedures are described for the evaluation of the equilibrium constant (or constants) and the BAB or BBA terms. It appears that this procedure is a general one which is applicable to associations of the type nA + mB ⇄ AB + A2B + AB2 + …. By correcting for nonideal behavior, one should then be able to apply it to any method available for analyzing ideal associations of the types considered here. In addition it is possible, subject to certain restrictions, to analyze associations of the type 3A + B ⇄ A2 + AB.
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    Biopolymers 7 (1969), S. 39-58 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method has been developed for characterizing at, submicrogram levels the heterogeneity of histones from purified nuclei. The histones are eluted with a smooth concentration gradient from nuclei trapped in polyacrylamide-gel threads and are collected in a micro fraction collector suitable for volumes in the 10-100 μl range. The gradient and fraction collection systems are governed by cam driven syringes. Samples obtained are subjected to electrophoresis in a starch-gel system and the gels are stained with a highly sensitive stain specific for guanidinium groups. Seven major and a similar number of minor components are demonstrated in the histones. The method of differential elution of trapped macromolecules is suitable for use with systems other than nuclei and histones.
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    Topics: Chemistry and Pharmacology
    Notes: A method is presented for the treatment of distribution functions obtained by ultra-centrifugal sedimentation velocity experiments on the plasma lipoproteins, so that adequate corrections can he made for the effects of diffusion and concentration dependence of the sedimentation coefficient. The method involves the use of modified equations derived from those presented in 1952 by Gosting for the transform from g* (S) to g(S) distributions. The evaluation of the molecular parameters of lipoprotein density and size, from a set of g(Si°) distribution functions obtained in solvents of varying density, is also outlined. Preparations of the β-lipoprotein of human plasma are found to follow a bivariate normal distribution that requires evaluation of five parameters, x̄1, σ1, x̄2, σ2and p. The first two represent the mean and standard deviation of the lipoprotein density, the third and fourth the same quantities for the size, expressed as ft “logarithmic diameter parameter”, and the final value is a measure of the correlation between these two variables.
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    Biopolymers 7 (1969), S. 133-133 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 7 (1969) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 7 (1969), S. 155-171 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: High-resolution nuclear magnetic resonance spectra at 100 MHz and 220 MHz have been obtained on two samples of poly-L-alanine of differing molecular weights (2500 and 42 500) in the chloroform-trifluoroacetic acid system under various conditions of solvent composition, temperature, and polypeptide concentration. Separate helix and random coil peaks are observed for the α-CH and peptide NH backbone proton resonances, thereby permitting the determination of helix content. This observation of separate peaks demonstrates that the lifetimes of the helix and random coil portions of poly-L-alanine have lower limits of about 10-1 sec. It is suggested that solvent-peptide versus peptide-peptide hydrogen bond competition, coupled with a destabilizing effect of the trifluoroacetic acid on the helix, is responsible for the helix-random coil transformation.
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    Biopolymers 7 (1969), S. 135-153 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The combination of an agarose gel (Bio-Gel A) and a dioxane-water (1:1) solvent system allowed the fractionation, on a preparative scale, of a very polydisperse, non-derivatized lignin preparation (enzymatically liberated lignin prepared from sweetgum sapwood with Lenzites trabea). Three fractions differing markedly in molecular weight were obtained. A gel of crosslinked alkylated dextran (Sephadex LH-20) with the same solvent system allowed division of the lowest molecular weight fraction into two fractions. These materials were characterized by measurements of intrinsic viscosity and number-average molecular weights in dimethylformamide and dioxane-water. It was established that the two highest molecular weight fractions were associated in an average trimeric form in dioxane-water (1:1) as compared to the form (considered to be molecular) that occurred in dimethylformamide. Molecular size distributions and eluant volumes of the fractions were determined with a Sephadex G-100-formamide system, the latter being one of the most powerful nonaqueous solvents for lignin. Adsorption effects were known to be absent in this case, and the lignin molecules were considered to be unassociated in formamide. The four fractions were distinguishable with the formamide-G-100 system, thus indicating that the original fractionation was based on molecular size. The enzymatically liberated lignin contained molecules that comprised a continuum of molecular weights from approximately monomeric to molecules that were at the limit of the solvating power of dioxane-water (1:1) and dimethylformamide. Limited physicochemical data were consistent with a compact, approximately spherically symmetric shape of the lignin in solution.
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    Biopolymers 7 (1969), S. 189-197 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparison has been made of the intrachain potential energy of an infinite straight α-helix of poly-L-alanine with that of the distorted form adopted in a coiled coil conformation. The energy terms included were the van der Waal's, electrostatic, hydrogen-bond, and the rotational potential terms. The results indicate that the potential energies of the structures investigated are almost the same, and so a transformation from one state to another may occur without significant changes in potential energy. Particular care has been taken to ensure that the electrostatic and van der Waal's interaction terms are fully convergent. The values obtained for the α-helix were compared with those already published, and some significant differences were found.
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    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet optical rotatory dispersion curves of mucopolysaccharides exhibit particular Cotton effects in the spectral region of the n-π and π-π amide transitions. Two general patterns emerge: (1) enhancement of negative rotation and of the first negative Cotton effect (troughs 217-220 mμ) and (2) relative dominance of the positive Cotton effect in the π-π transition region (peak ∼198 mμ). Groups (1) and (2) can be correlated with a structural difference in the linkages of the amino sugars: (1) occurs with polymers containing 3-1-linked glycosamino sugars and (2) with glycosamino moieties linked 4-1 by either α- or β-glycosidie bonds. Measurements of the circular dichroic absorption bands support the qualitative conclusions from optical rotation. All mucopolysaccharides exhibit a first, negative band centered at 208-211 mμ, while only those in group (2) show, in addition, a positive band centered at 189-192 mμ. A suggested unifying model considers that difference in kind and/or degree of preferred geometry of the amide groups obtains from two forms of secondary order: (1) having a linear hydrogen bond from the N (acceptor) to the (C2)O - H of the preceding uronic acid and (2) having a linear hydrogen bond from the N (acceptor) to the (C2 or 3) O - H of the following sugar. The hydrogen bonds would have similar strength but opposite directions in two systems towards the nonreducing end (1) or towards the reducing end (2)], closing eight-membered rings
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    Biopolymers 7 (1969), S. 99-106 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The myosin molecule was extracted from the smooth muscle parts of horse esophagus and purified by ammonium sulfate fractionation. The schlieren pattern of the sedimentation velocity run showed a very sharp single peak of.5.9. S (s20,w). Molecular weight of the protein was measured by means of the Archibald and sedimentation equilibrium methods, both in 0.5M KCI buffered by 1/150 M phosphate at pH 7.5 and at 5°C. The values obtained were 6.25 × 105 and 5.81 × 105respectively, for the two methods. The second virial coefficients were 1.1 × 104 and 1.2 × 10-4 ml/g. Denatured smooth muscle myosin was prepared in a solution of 5M guanidine HC1 containing 0.4 M KC1 and 0.2 M β-mercaptoet hanol buffered at pH 8.0. The weight-average molecular weight of the denatured smooth muscle myosin was 2.24 × 105 and the second virial coefficient was 7.6 × 10-4 ml/g. The values described above are in good agreement with those reported for rabbit skeletal myosin with ammonium sulfate fractionation. The molecular dimension of the molecule is estimated as the value for an axial ratio of 100, assuming a rigid rod molecular model for this molecule, both the thermodynamical and hydrodynamical treatment being in a good agreement with this estimation.
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  • 85
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    Biopolymers 7 (1969) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 86
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    Biopolymers 7 (1969), S. 433-434 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No. Abstract
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  • 87
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The enthalpy change accompanying the double helix-coil transition of polyriboadenylic acid (poly A) in aqueous solution has been measured optically and calorimetrically in the pH range 5.7-4.5. The course of this cooperative transition was followed optically by measuring changes in ultraviolet absorption as a function of temperature at different pH values, and calorimetrically by determining the heat capacity of the solution through the transition region. From the latter measurements, the enthalpy of transition was calculated. It is shown, that ΔH is dependent on pH as it is expected from the influence of protonation of the double helix of poly A.
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  • 88
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    Biopolymers 7 (1969), S. 453-458 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction between ionizable carboxyl groups and the conformation of poly-(glutamic acid) (PGA) in aqueous solution were investigated by the mechanical method. The dynamic rigidity of the PGA solution has a maximum value at the pH corresponding to about 50% neutralization point. This may be due to establishing of a maximum attractive force by proton/charge fluctuation between ionizable carboxyl groups at that pH. The dynamic viscosity has a sharp change in the region of pH 5.5-6.5. It is suggested that this behavior is due to the helix-coil transition.
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  • 89
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    Biopolymers 7 (1969), S. 447-452 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: By use of D2O we found that the shortening of the longitudinal proton relaxation time which occurs in the investigated aqueous yeast DNA solutions (≦ 2.4% with 2% protein) was not based on a hydration effect, but was caused by magnetic impurities only. An estimate shows that the mobility of the hydrated water molecules is reduced by less than two orders of magnitude in comparison with the free water molecules.
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  • 90
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    Biopolymers 7 (1969), S. 435-445 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general approach to the determination of relative stability of any pair of con-formational states of biological macromolecules or their complexes (in particular, to the determination of relative stability of native and disordered states of the macromolecule) has been suggested. For determining the free energy difference of the two states under the conditions when one of them is considerably more advantageous than the other, it is necessary for the macromolecule to be influenced by the transforming agent which levels free energies of both the conformational states, and to determine the external parameter derivative of the free energy difference in the region of the conformational transition induced by the change in this parameter. If the character of the dependence of this derivative on the external parameter (temperature, solvent composition, etc.) is known, then this allows the determination of the free energy difference of the two states under the conditions considered, even including conditions far from the transition region. The value of the derivative of the free energy difference in the transition region in many cases can be measured directly (in particular, when using calorimetry), while in cases when a direct measurement of the derivative is impossible, it can often he estimated experimentally from the steepness of the conformational transition. The methods of this estimation and also a possible character of the change of the considered derivative during variation of the external parameter are considered for the case when the transforming agent is one of the components of the solvent and, consequently, the derivative of the free energy difference is equal to the difference of number of molecules of this component hound with the macromolecule in two conformational states.
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  • 91
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    Biopolymers 7 (1969), S. 459-474 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Wool-water systems, at water contents above a threshold value of 22.7 g of water per 100 g of wool keratin, yielded curves of specific heat against temperature showing peaks that are ascribed to the fusion of the absorbed water. Integral and incremental heats of fusion were obtained. Integral heats increase as the square of the water content above the threshold, and incremental heats follow a linear relationship. The incremental heat reaches a value of 55 cal/absorbed water, at the saturation water content, at 0°C of 33.9 g of water per 100 g of keratin. The state of the absorbed water is discussed. Clustering of water molecules takes place only above the threshold water content.
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  • 92
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    Biopolymers 8 (1969), S. 173-179 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The laser-excited Raman spectra have been obtained of poly-L-proline in the solid and aqueous solution. In the solid state, the Raman spectra are of the form II which is the left-handed helical form with the peptide bonds in the trans configuration. Dissolution of this form in water produced only minor changes in the Raman spectra. The differences in frequencies produced by dissolving the polymer are associated with vibrational modes of the pyrrolidine ring as indicated by comparison with the Raman spectrum of L-proline. The similarity of the Raman spectra dictates that, the conformations of poly-L-proline chain are similar in the solid and aqueous solution.
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  • 93
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    Biopolymers 8 (1969), S. 181-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparative study on sonicated calf thymus DNA was made by using electron microscopy and sedimentation methods. The length distribution, established by electron microscopy by using Kleinschmidt's technique, is related to the sedimentation curve obtained with the same solution. The relation permits a determination of the sedimentation constant corresponding to a given length up to 8000 Å and vice versa.
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  • 94
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    Biopolymers 8 (1969), S. 199-216 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The π-electron polarizability of conjugated base molecules such as uracil and adenine are calculated semiempirically by using molecular orbital theories. The Hüekel method and the self-consistent-field (SCF) theory are used in the present calculation. The theoretical values obtained by the Hüekel method are consistently larger than the experimental results. The values obtained by the SCF theory are in good agreement with observed values. It is clearly demonstrated that the SCF method is better than the Hükel method for the calculation of polarizability. The polarizability of the adenine-uracil pair is calculated as the sum of the polarizabilities of adenine and uracil and also calculated by solving the eigenvalue problem for the A-U pair as an entity. The second method gives considerably larger polarizability than the first method. Discussions are presented and it is demonstrated that the second method is the correct way to calculate the polarizability of the A-U pair.
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  • 95
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reversibility of the thermal denaturation of a low-sulfur fraction of solubilized wool keratin (SCMKA) has been studied under a variety of conditions of time, protein concentration, and pH. Two types of irreversibility for the transition have been encountered. One of these is associated with an aggregation of the protein on denaturation to give a product which may contain elements of a β conformation. This type of irreversibility is favored by high protein concentration, and the original conformation may in fact be regained if the aggregated structure is broken down by a solvent such as 8M urea and the urea subsequently removed by dialysis. The other type of irreversibility appears to be due to racemization of the protein. It does not seem to be dependent on protein concentration and is apparent only at temperatures beyond the actual transition range (∼40-65°C) at pH values below 11, At pH 12, however, racemization appears to proceed slowly even at 4°C. The thermal transition at pH 9 and pH 10 has been shown to be multistage in nature. Over the pH range 9-12 there is a progressive decrease in thermal stability with increase of pH. Addition of NaCl at pH 10 leads to an increase in thermal stability of the molecule.
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  • 96
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    Biopolymers 8 (1969), S. 217-235 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report studies of the optical properties of the proflavine-DNA complex, using absorbance and circular dichroism spectroscopy. From comparison of the absorption spectra of proflavine complexed with calf thymus and T2 DNA, we conclude that stacking of the dyes external to the double helix is comparatively much weaker with T2 DXA, probably because of its glucosylation. Several sources are found for the circular dichroism induced in proflavine when it is complexed with DNA. There is a relatively weak circular dichroism induced when the dye is infinitely dilute on the DNA lattice; this presumably arises from the environmental asymmetry of the binding site. Stronger circular dichroism effects are induced by interaction of intercalated and stacked dyes; studies with T2 DNA, for which stacking seems to be blocked, permit a tentative resolution of effects due to the two modes of binding. One recurring theme of these studies is the observation that the optical properties are quite dependent on environment. The most dramatic example is a strong variation with salt concentration of the amplitude of the circular dichroism induced in the isolated (intercalated) monomer by the surrounding DNA. This suggests that the structure of the intercalated complex is quite sensitive to external conditions.
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  • 97
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of n-butanol, benzyl alcohol, and trifluoroethanol to polyproline I (all peptide bonds in cis configuration) and II (all peptide bonds in trans configuration) has been demonstrated. It was found by infrared spectroscopy that hydrogen bonds are formed between the CO groups of the polymer and the OH groups of the alcohols. Their strength increases from n-butanol via benzyl alcohol to trifluoroethanol. The binding of benzyl alcohol could also be followed by optical rotatory dispersion due to the fact that the electronic transitions of the benzyl ring are rendered optically active by the binding to the polymer.
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  • 98
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    Biopolymers 8 (1969), S. 259-274 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The statistical mechanics of the effect of a small number of randomly occurring defects on the melting of a polypeptide chain is developed by using a perturbation of Boltzmann factors technique. The method is illustrated by an example where a second-component impurity contributes more to the energy of the hydrogen-bonded superstructure of the polypeptide chain than does the dominant amino acid residue, resulting in the overall destabilization of the helical conformation.
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  • 99
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    Biopolymers 8 (1969), S. 275-287 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Biological membranes consist mainly of lipids and proteins. At present, the structure of the lipid phase appears to be established, but hypotheses on the molecular organization of the protein are difficult to support. Thus the deformation behavior of whole human erythrocyte ghosts, ghosts after the selective removal of lipids and ghosts stripped of lipids as well as nonlipid components have been examined in the hope of securing indirect information on the organization of the protein. It has been found that large localized deformations result in partial membrane failure and long uniformly wide fibrils, frequently in excess of 3000 Å, are drawn across the rupture. These data are interpreted in terms of currently favored membrane models and the possibility of a fibrous membrane framework consisting predominantly of protein is reviewed. The behavior of the membrane in its various stages of extraction is compared and contrasted to that of synthetic polymer films of known organization.
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  • 100
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    Biopolymers 8 (1969), S. 247-257 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermally induced conformational changes of poly-N5-(3-hydroxypropyl)-L-glutamine in water and in methanol-water (3:7 v/v) have been analyzed in terms of the Lifson-Roig theory. The transitions in both solvents can be described by using v = 0.017. The thermodynamic parameters for the random coil-to-helix transition of one amino acid residue at room temperature were found to be: in water, ΔH = - 130 cal/mole and ΔS = - 0.45 e.u.; in methanol-water (3:7 v/v), ΔH = - 170 cal mole and ΔS = - 0.45 e.u. The size distribution of helical segments is broad, and the results of numerical calculations are presented for three degrees of polymerization (DP = 100, 300, and 750).
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