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  • Polymer and Materials Science  (5,997)
  • Organic Chemistry  (1,315)
  • Physics  (1,112)
  • Chemical Engineering  (1,065)
  • Wiley-Blackwell  (8,377)
  • Institute of Physics
  • 1985-1989
  • 1980-1984  (8,377)
  • 1925-1929
  • 1984  (4,304)
  • 1980  (4,073)
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  • 1985-1989
  • 1980-1984  (8,377)
  • 1925-1929
Year
  • 101
    Electronic Resource
    Electronic Resource
    Adsorption of polypeptides on the solid surface. II. Effect of secondary chain structure and helix-coil transition (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 805-821 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The theory of adsorption of semistiff chains on a planar surface developed by the authors previously has been used to consider the helix-coil transition in single-stranded macromolecule interacting with an adsorbent plane. The cases of nonselective interaction when the adsorption energy is independent of the unit conformation (a) and selective interaction with only helical (b) or coiled (c) sequences active in adsorption were investigated. In case (b) the existence of secondary structure favors chain bonding to the surface. This leads to the increase in the stability of the helical state and complete polypeptide chain spiralization. The profile of the conformational helix-coil transition acquires an asymmetrical shape inherent to the second-order phase transition.In case (c) the bonding of a partially helical chain to the surface is similar to the adsorption of Gaussian coils and is accompanied by the destruction of secondary structure, this destruction being appreciable even if the helical state in space was favorable.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190407
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  • 102
    Electronic Resource
    Electronic Resource
    Unwinding of DNA induced by fluorescein mercuric acetate (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 991-999 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fluorescein mercuric acetate causes the unwinding of DNA and binds to the separated bases. This unwinding process can be followed by measuring absorption changes of this reagent. For untreated calf thymus DNA, the initial rate was very slow, and the shape of the kinetic curve was sigmoidal. When double-strand breaks of DNA were produced by DNase II treatment or sonication, the initial rate increased and the sigmoidal character disappeared. The initial rate was shown to be proportional to the concentration of helix ends. From this relation the rate of unwinding was estimated to be 2.0 base pairs/sec at 1.0 × 10-5M fluorescein mercuric acetate and 25°C. DNase I treatment, which produces single-strand breaks and a smaller number of double-strand breaks, also increased the initial rate. However, this increase was due only to the double-strand breaks, that is, single-strand breaks had no significant effect on the initial rate. Also, uv irradiation increased the initial rate linearly with uv dose, at least up to 2 × 105 erg/mm2, suggesting that this increase is due to photoproducts other than usual pyrimidine dimers. We discuss the usefulness of this kinetic method in structural studies of DNA.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190505
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  • 103
    Electronic Resource
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    Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′-deoxyadenosine CD spectra (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1017-1038 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A combination of the DeVoe and Kirkwood polarizability concepts is developed to calculate CD spectra of nucleic acid monomers. The method is perfectly general and applies to any system where the constituents have absorption properties which are widely separated in terms of frequency. The theory is applied to calculate the CD spectra of adenosine and 2′-deoxyadenosine conformers. Bond polarizabilities are evaluated for the ribosyl moiety of adenosine, as a function of glycosidic rotational angles and polarizability anisotropies. It is found that a wide range of C-C and C-O bond polarizabilities give similar CD results. Isotropic atom polarizabilities are also evaluated. It is found that the CD results using these polarizabilities do not differ significantly from those obtained with bond polarizabilities. The CD spectra of adenosine and 2′-deoxyadenosine are calculated for three x-ray diffraction determined geometries: A-form RNA, B-form DNA, and C-form DNA. The results indicate that the monomer CD spectra are strongly dependent on the precise geometry and appear to be of importance in understanding the spectra of oligomers and polymers. The deoxyadenosine conformers are found to have calculated CD spectra which are less intense than those of the ribosyl conformers. These results indicate that the measured differences between the CD magnitudes of ribo- and deoxyriboadenosine are due to the presence or absence of the 2′-hydroxyl. Weighted averaged adenosine CD spectra are calculated with the aid of probability distributions from conformational energy calculations. The results suggest a new method for obtaining empirical monomer parameters for use in optical calculations. The calculations in this paper indicate for the first time that DeVoe theory, in combination with the Kirkwood theory, provides a useful method for the calculation of the CD spectra of nonpolymeric molecules.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190507
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  • 104
    Electronic Resource
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    β-Chain conformation of the high-sulfur proteins from wool (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1093-1097 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190512
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  • 105
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    Calorimetric determination of the enthalpy of ionization of oxidized and reduced horse heart cytochrome c (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 899-911 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The heats of ionization of protons, ΔHi, of oxidized and reduced horse heart cytochrome c in 0.15M KCl at 20°C were determined using a titration calorimeter which simultaneously afforded the potentiometric titration curve. Reproducibility of the thermal titrations is within 2%, and evaluation of the heats observed after the heat loss corrections is estimated to be within 5%. A single titration of oxidized cytochrome c from pH 11 to 3 is in excellent agreement with the thermal titration of this protein obtained with flow calorimetry. The thermal titration, however, is not reversible, due in part to the loss of titratable group(s) in this pH region and to the heat contribution of the acid and alkaline conformational changes which occur. Although of lesser magnitude, the reduced form also indicates similar thermal transitions. These differences are due solely to conformational contributions to the thermal process, since the potentiometric curves are reversible. The nature of the irreversibility for oxidized cytochrome c appears to involve the loss of a group with pK′ 8.9 and the shift of two groups from pK′ 5.6 to 4.8. Thermal difference curves for this process indicate that heats of -7.8 and -24.1 kcal/mol are liberated which are centered at pH 9.3 and 3.9, respectively.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190413
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  • 106
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    Syn-anti equilibrium of purine bases in dinucleoside monophosphates as studied by proton longitudinal relaxation (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1211-1239 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preferential orientations of the purine bases in dinucleoside monophosphates such as ApA, ApG, and GpA in 10-2M neutral aqueous solutions have been investigated by proton relaxation at 250 MHz. These orientations are deduced from computer simulations of the magnetization recovery curves following a 180° nonselective pulse. The distances between the H(8) proton of a base and the ribose ring protons which are used in these calculations are obtained by minimization as a function of the glycosyl torsion angle ϒ of the standard deviation between the isotropic reorientation correlation times τR derived from the relaxation rates of these protons. The average H(1′) - H(8) distance obtained by this procedure may be readily verified from the reduction of the H(1′) relaxation rate when H(8) is substituted by a deuteron. The limits of validity of the assumption of a single correlation time τR governing the proton relaxation have been estimated, taking into account several possible internal motions, e.g., the rotation of the base, of the methylene exocyclic group and the N ⇄ S interconversion of the ribose ring. For 10-10 〈 τR 〈 2 × 10-10 sec, it appears that the influence of these motions on the proton relaxation becomes perceptible when the jump rates among equilibrium positions exceed ca. 109 sec-1.The whole of the experimental results show that for the ribose ring N conformer, the orientation of the bases is found in the ranges 60° 〈 ϒ 〈 80° (syn) and 180° 〈 ϒ 〈 210° (anti). For ribose S conformer, it is observed that this orientation is mainly syn with 5° 〈 ϒ 〈 90°. The average H(1′) - H(8) distance provides semiquantitative information on the overall syn or anti orientations of the base in each nucleoside moiety. At 298 K the population of the anti conformer is found to increase in the order A- pG 〈 Ap-G ∼ Gp-A 〈 Ap-A 〈 A-pA 〈 G-pA. A more detailed analysis of relaxation data shows that the maximum possible fraction of the stacked form of dinucleotides, due to the occurrence of N-anti conformers in both nucleoside moieties, is in the order ApG 〈 GpA 〈 ApA, in agreement with previous works, with however smaller values.Lastly the deuteron linewidth in position 8 of the bases indicates a syn-anti transition rate of the order of 109 sec-1 at room temperature, without noticeable effects therefore on the proton relaxation.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190608
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  • 107
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    Effect of counterions on complex coacervation (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1289-1298 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In a recent paper, we developed a thermodynamic theory on the complex coacervation in the absence of low molecular ions, under the assumption that the coacervation is a condensation phenomenon of aggregates of polyanion and polycation in the aqueous solution, by obtaining the interaction potential US between these aggregates on the basis of Flory's method. In this paper, we have extended the theory to a more complicated phenomenon of the counterion-containing solutions. This treatment has led the interaction potential having an additional contribution to US resulting from an entropy increase by the counterion distribution. The phase diagram between solution (sol) and separated phase has been obtained as a function of the difference of charges between polyanion and polycation. It has been found that the presence of counterions sensitively suppresses the coacervation.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190705
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  • 108
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    Dielectric relaxation of DNA solutions. IV. Effects of salts and dyes (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1039-1047 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of salts (NaCl, LiCl, Me4NCl, AgNO3, MgCl2, CuCl2 and MnCl2) and dyes (acridine orange and methylene blue) on the low-frequency dielectric relaxation (0.1 Hz-30 kHz) of dilute aqueous solutions of DNA were investigated with varying salt or dye concentrations. Both the dielectric relaxation time τD and the rotational relaxation time τ estimated from the reduced viscosity decrease in quite parallel ways with increasing M/P (M/P being the normality ratio of cation to phosphate residue), reflecting the contraction of DNA molecule due to electrostatic shielding and cation binding. The agreement between τD and τ through the whole range of M/P supports our previous conclusion that the low-frequency relaxation of DNA arises from rotation of the molecule. The dielectric increment Δε also decreases with increasing M/P on account of both the contraction of DNA and the decrease in effective degree of dissociation of DNA. Δε as a function of M/P is interpreted in terms of a quasi-permanent dipole due to counterion fluctuation. These effects of cations are the strongest for divalent cations and rather weak for Na+, Li+, and Me4N+. Effects of dye on τD and Δε are also well explained by the rotation of DNA molecule with a quasi-permanent dipole due to counterion fluctuation on the basis of intercalation of dye at D/P 〈 0.2 (D/P being the molarity ratio of dye to phosphate residue) and external binding at 0.2 〈 D/P 〈 1.0.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190508
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  • 109
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    Models for boundary effects on molecular rotation in membranes (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1597-1602 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rotational and wobbling diffusion coefficients for spherical and long-chain molecules in membranes are calculated using a simple hydrodynamic model. Estimates of the contributions to the diffusion coefficients arising from hydrodynamic interactions between molecules and membrane interfaces are obtained and found to be small. For molecules containing polar head groups, we show that the presence of a membrane interface can produce a significant reduction in the wobbling diffusion coefficient over what would be obtained in an isotropic fluid.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190904
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  • 110
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    Cation effects on the nonlinear electrical properties of DNA solutions (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1629-1640 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nonlinear electrical properties of DNA solutions were measured when different monovalent cations were added to DNA. The influence of different parameters has been examined: fundamental frequency, field strength, and concentration. A linear relationship between the harmonic current Ih and the DNA concentration is shown, even for higher concentration values (400 mg/l.). The frequency dispersion of Ih has the same shape for all the cations and the low-frequency amplitude of Ih increases in the following order: Li+ 〈 Na+ 〈 K+ 〈 NH4+ 〈 Cs+. The nonlinear polarizability values are compared with the linear ones determined using the very low field electric birefringence technique. Both linear and nonlinear values are of the same order of magnitude. It is thought that the nonlinear electrical property of high-molecular-weight DNA mainly results from the deformation of the DNA coils by the electric field.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190907
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  • 111
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    Dependence of the internal relaxation time for DNA on salt type as inferred by quasielastic light scattering (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1655-1666 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quasielastic light scattering methods were used to study calf thymus DNA in solutions of LiCl, NaCl, NH4Ac, and NH4Cl. Plots of the reciprocal relaxation time (1/τ) vs sin2(θ/2), where θ is the scattering angle, exhibit two linear regions, in accordance with theories for semiflexible polymers based on the t → 0 approximation. In these theories the slope of the linear region at low angles is associated with the translational diffusion coefficient (Dt), whereas the slope of the linear region at high angles is associated with the segmental diffusion coefficient (Ds = kT/ƒs). The midpoint of the “transition” between these two linear regions is associated with the mean displacement between segments (b). Data presented here indicate that the Rouse-Zimm parameters b and ƒs are significantly different for DNA in 0.4M NH4Cl relative to the other salts at comparable ionic strengths. It is suggested that this difference reflects local solvent structure and that both b and Ds are sensitive to the local water structure.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190909
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  • 112
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    Microscopic persistence length of native DNA: Its relation to average molecular dimensions (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1689-1694 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190912
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  • 113
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    Effect of some monohydric alcohols on the oxygen affinity of hemoglobin: Relevance of solvent dielectric constant and hydrophobicity (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1703-1703 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190914
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  • 114
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    Masthead (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191001
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  • 115
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    Sodium counterion activity of poly(S-carboxymethyl-L-cysteine) and the beta-random-coil transition (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1743-1752 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Sodium ion activity was measured using a Na-glass electrode in a solution of poly(S-carboxymethyl-L-cysteine) with no added salt at various degrees of neutralization and various concentrations for samples of different molecular weights. The conformational change from random coil to the β-structure was detected from the activity coefficient of counterions, as well as from CD. At a constant degree of neutralization, the activity coefficient is insensitive to a concentration change not only in the random-coil state, but also in the range of conformational change if the concentration is below about 3 × 10-2 monomolal. At high concentrations of about 5 × 10-2 monomolal, however, the activity coefficient becomes low, probably due to the occurrence of the stacking of the pleated sheets.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191005
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  • 116
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    1H-nmr study of protected methionine homo-oligopeptides in helix-supporting environment (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1791-1799 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-nmr spectra for a series of Boc-L-(Met)n-OMe (n = 2-9) homo-oligopeptides have been observed in the helix-supporting solvent trifluoroethanol (TFE) at millimolar concentrations. Interfering solvent peaks were eliminated using two decoupling frequencies to selectively remove the methylene and hydroxyl protons of the solvent. Comparisons with specifically α-deuterated homo-oligopeptides gave complete assignments of the NH region of the Boc-Metn-OMe oligomers up to the heptapeptide. Analysis of chemical shifts, coupling constants, and temperature dependence of chemical shifts suggests that up to the hexapeptide, similar structures exist in deuterochloroform and TFE. In contrast, nmr parameters at the heptapeptide for several internal residues differ in these solvents. These results suggest that a C7 to α-helix transition may occur in TFE as the chain length of the methionine oligopeptides increases.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191008
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  • 117
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    Use of natural-abundance 15N-nmr spectroscopy to investigate the secondary structure of peptides: Gramicidin S (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1815-1826 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The natural-abundance 15N-nuclear magnetic resonance (nmr) spectrum of the cyclic decapeptide gramicidin S has been measured and assigned in the solvents dimethyl sulfoxide, methanol, and 2,2,2-trifluoroethanol. Three methods have been investigated to distinguish between peptide groups which are exposed to or shielded from the solvent. The solvent dependence of the 15N chemical shift is correlated with the two types of peptide group in gramicidin S—those with the carbonyl group exposed or shielded from the solvent. The second method monitors the lability of the N—H proton (via the collapse of the reduced 15N-1H coupling) in the presence of added base used to promote intermolecular exchange - peptide protons shielded from the solvent exchange more slowly. The third method looks at the temperature dependence of the 15N chemical shifts in dimethyl sulfoxide. Here the data are not so distinctive as to allow the differentiation between solvent-exposed or shielded N—H bonds at all peptide groups.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1980.360191010
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  • 118
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    Modification of the apparent radius of gyration of cytochrome c by the distribution of counterions in solution (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1887-1897 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small changes in the apparent radius of gyration of native cytochrome c were measured as a function of pH in solutions of 0 and 50 mM ruthenium hexicyanide. The forward scattering was also measured as a function of pH under the same conditions to ascertain the contribution of the Ru ion shell to the forward scattering and concomitantly to the radius of gyration. The forward scattering and small alterations in the radius of gyration were then measured as a function of Ru counterion concentration. These results are then interpreted in terms of the mechanisms which influence the measured apparent radius of gyration. It is shown that the Debye-Hückel theory of counterion distributions can be used to describe the data in situations where scattering from the bound Ru ions contributes less significantly than scattering from the ion cloud.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191015
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  • 119
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    Masthead (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191101
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  • 120
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    Fluorine nmr studies of poly(N-acryloyl-β-alanine)-α-chymotrypsin conjugates (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1827-1837 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fluorine nmr experiments carried out at 51.0 and 94.1 MHz have been used to explore the interaction of the probe molecule p-fluorocinnamate with conjugates formed from α-chymotrypsin and poly(N-acryloyl-β-alanine). The data obtained include enzyme-induced chemical-shift effects, spin-lattice (R1) and transverse (R2) relaxation rates, and the rate constant for dissociation of the fluorocinnamate-enzyme complexes. Analysis of the results indicates that while overall molecular tumbling of the enzyme molecule is not greatly changed by attachment of polymers of various sizes, conjugated polymer can appreciably affect the structure of the p-fluorocinnamate binding site. The important variable involved in such structural changes appears to be the amount of polymer present per mole of protein.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191011
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  • 121
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    Concentration distribution and spatial moments of moving macromolecules undergoing isomerization (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1875-1886 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Expressions for zeroth, first, and second spatial moments are obtained for diffusing macromolecules A and B that move due to an external field and undergo reversible isomerization, switching back and forth according to first-order kinetics. In addition, expressions for third and fourth moments are derived for the special case of equal diffusion coefficients, equal rate constants, and equal but opposite velocities. The initial conditions are arbitrary amounts of A or B concentrated in an infinitesimally narrow region. The moments are computed from derivatives of the Fourier-transformed concentration profiles of A and B. The moments are used in an expansion in term of Hermite polynomials, the Gram-Charlier expansion, to construct the concentration profiles of A or B or A and B together. The examples presented show that a few terms of the expansion, for which explicit expressions are given, can give tolerable accuracy if the velocity is not too large and the rate constants and diffusion coefficient are not too small. The expansion can be used to determine when the profiles are unimodal.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1980.360191014
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    Triple helix-coil transition of covalently bridged collagenlike peptides (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1909-1917 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermal triple helix-coil transition of covalently bridged collagenlike peptides with repeating sequences of (Ala-Gly-Pro)n, n = 5-15, was studied optically. The peptides were soluble in water/acetic acid (99:1) and were found to form triple-helical structures in this solvent system beginning with n = 8. The thermodynamic analysis of the transition equilibrium curves for n = 9-13 yielded the parameters ΔH°s = -7.0 kJ per tripeptide unit, ΔS°s = -23.1 J deg-1 mol-1 per tripeptide unit for the coil-to-helix transition, and the apparent nucleation parameter σ ≃ 5 × 10-2. It was suggested through double-jump temperature experiments that the rate-limiting step during refolding is not only influenced by the difficulties of nucleation, but also by cis-trans isomerization of the Gly-Pro peptide bond.
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    Experimental characterization of poly(hydroxyalkyl-L-glutamine) conformations in aqueous calcium chloride and sodium perchlorate solutions (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1923-1941 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly(hydroxyalkyl-L-glutamine) (alkyl = ethyl, propyl, butyl) solutions have been studied by CD as functions of temperature and activity of calcium chloride and sodium perchlorate. Helical content is altered by changes in salt activity and temperature. The helicity of poly(hydroxybutyl-L-glutamine) and poly(hydroxypropyl-L-glutamine) falls to zero in a monotonic fashion with increasing calcium chloride activity. A nonzero helicity reappears at activities in excess of 5-50 mol kg-1. Poly(hydroxypropyl-L-glutamine) is much more sensitive to calcium chloride than is poly(hydroxybutyl-L-glutamine), and both polypeptides are more sensitive to calcium chloride than are typical proteins. Markedly different behavior is observed with sodium perchlorate. This salt acts as a helix stabilizer at low activities but becomes a destabilizer at activities higher than 0.3-1.0 mol kg-1. In this respect the effect of sodium perchlorate on nonionic poly(hydroxyalkyl-L-glutamines) resembles that seen with cationic poly(L-lysine) and poly(L-arginine). Helix stabilization at low sodium perchlorate activity is moderate for poly(hydroxybutyl-L-glutamine) and large for poly(hydroxypropyl-L-glutamine) and poly(hydroxyethyl-L-glutamine).
    Additional Material: 16 Ill.
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    Influence of uracil photohydrate formation on the conformational properties of heterodinucleoside monophosphatesA preliminary account of some of this work was presented at the 21st Annual Meeting of the Biophysical Society, New Orleans, Louisiana; Symposium abstracts in Biophys. J. (1977) 17, 223a. (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1983-2002 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structural properties of uracil photohydrates at the monomer and dimer level in aqueous solution have been examined in detail by nmr spectroscopy. Based on such evidence, the absolute configurations of the two possible diastereomers have been assigned, and the conformational perturbations induced by photohydration have been evaluated. In all instances, photohydration shifts the 2E ⇌ 3E puckering equilibrium of the sugar ring of the uridylyl fragment towards 2E (from 12-18%). In addition, for both dimers examined in detail, ho6UpA and Apho6hU, the effect of dimerization on sugar pucker is such that the 3′-terminal unit shows a clear increase in the percentage of 3E (relative to the appropriate 5′-mononucleotide), whereas the percentage 3E of the 5′-terminal unit shows no change. This is contrary to the findings in the normal dinucleoside monophosphates, where an increased preference for 3E pucker occurs in both residues on dimerization and increased base stacking. Significant base-base interactions were observed in both hydrated dimers despite the loss of the planar π-system in the uracil fragment. In addition, the rate of photohydration for a particular dimer pair (e.g., ApU and UpA or GpU and UpG) is shown to be inversely dependent on the amount of base stacking in the parent dimer. This latter parameter has also been correlated with the ratio of the two possible diastereomers formed in the reaction and is associated with a preferential attack at one face of the pyrimidine base ring. The shift of the sugar puckering equilibrium towards 2E has been compared with similar shifts observed when adenosine and guanosine are methylated at N(1) and N(7), respectively. The possible biological significance of the above-mentioned conformational aspects is discussed.
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    Helix-coil transitions in a simple polypeptide model (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2033-2045 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simplified model of a polypeptide chain is described. Each residue is represented by a single interaction center. The energy of the chain and the force acting on each residue are given as a function of the residue coordinates. Terms to approximate the effect of solvent and the stabilization energy of helix formation are included. The model is used to study equilibrium and dynamical aspects of the helix-coil transition. The equilibrium properties examined include helix-coil equilibrium constants and their dependence on chain position. Dynamical properties are examined by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Correlations in the motions of the residues are found to have an important influence on the helix-coil transition rates.
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    Electric dichroism and birefringence of poly(ribocytidylic acid). I. Optical properties and stability (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2123-2132 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements of the uv absorption and melting profiles of poly(rC) at low-salt conditions confirm the existence of a double-stranded complex at low pH and imply, but do not prove, the structure proposed by Akinrimisi et al. (1963) Biochemistry 2, 340-343. Electric dichroism and birefringence provide additional supporting evidence and indicate that the complex is one in which the bases are tilted considerably from the major molecular axis. The base-stacking tendency of single-stranded poly(rC), unlike poly(rA), is found to be insufficient to maintain a rodlike structure; the persistence length of stacked bases in poly(rC) must be very small. The existence of an out-of-plane transition in poly(rC) in the vicinity of 300 nm is conclusively demonstrated by both dichroism and birefringence measurements.
    Additional Material: 7 Ill.
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    Study of the influence of NH⃛S hydrogen bonds on the reduction potential in Clostridium pasteurianum 2(4Fe-4S) ferredoxin using deuterium exchange (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2133-2141 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of deuterium substitution of exchangeable hydrogen atoms on the reduction potential of Clostridium pasteurianum 2(4Fe-4S) ferredoxin has been studied. The studies were conducted to determine if NH⃛S hydrogen bonds to the iron-sulfur cluster are dominant in the mechanism of influence of the protein on cluster reduction potential, as has been proposed [Carter, C. W. (1977) J. Biol. Chem. 252, 7802-7811]. Deuteration of the slowly exchangeable hydrogen atoms, however, yields essentially no shift in the reduction potential (-0.2 ± 0.8 mV), suggesting that NH⃛S bonds are not important modifiers of cluster reduction potential in this protein.
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    Kinetics of reactions involving DNA containing stress-induced single-stranded regions (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2143-2164 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The theoretical kinetics are analyzed for reactions between torsionally stressed DNA and another compound which reacts at different rates with portions of the substrate molecule which are in different conformational states. These reactions are assumed to obey Michaelis-Menten kinetics, so no cooperative effects occur. The DNA is regarded as being susceptible to a stress-induced local conformational transition as described recently by Benham. Briefly, alterations in torsional stress consequent on superhelicity effectively change the relative concentrations of the two conformational states of the substrate, thereby influencing the course of the reaction. This theory is developed for transition between the B-form helix and the single-stranded, random-coil states. To illustrate the influence of posited stress-induced melting on kinetics, calculations are made on simple models of two biochemical phenomena. First, the variations in initial nicking rates of single-strand-specific endonucleases with substrate superhelicity are interpreted as arising from changes in the concentration of (stress-induced) single-stranded binding sites. Second, the observed dependence of the transcription rate of RNA polymerase core enzyme on substrate superhelicity is interpreted in terms of a model in which the rate-limiting step in the initiation event is the formation of a complex between the enzyme and a single-stranded region. Related experimental results are shown to be qualitatively consistent with the suggestion that sufficiently supercoiled DNA contains locally melted regions.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1980.360191202
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    A theory for polarized fluorescence microscopy of chromosome structures (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2267-2267 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360191209
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    DNA bis-intercalation: Theoretical calculation of binding curves (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 419-430 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A statistical mechanical calculation of the binding properties of DNA bis-intercalators is presented, based on the sequence-generating function method of Lifson. The effects of binding by intercalation of one or both chromophores of a bifunctional intercalating agent are examined. The secular equation for a general model that includes the effects of neighbor (nearest and non-nearest) exclusion and/or cooperativity in the binding of both singly and doubly intercalated ligands is derived. Numerical results for binding curves are presented for a more restricted model in which each type of bound ligand rigorously excludes its nearest neighbor and the total number of sites covered by a doubly intercalated ligand is variable. At low values of free ligand concentration bis-intercalation dominates the binding process, while at high value of free ligand concentration, intercalation of only one chromophore per ligand becomes significant due to the unavailability of contiguous free sites required for bis-intercalation. Also, depending on the binding parameters, the free energy of the system can be lowered by a loss of doubly intercalated ligands in favor of singly intercalated ones. Corresponding to this transition in binding mode, the average number of sites occupied by a bound ligand decreases from that characteristic of bis-intercalation to that characteristic of mono-intercalation as free ligand concentration increases. An analysis of Scatchard plots describing bis-intercalation is presented.
    Additional Material: 7 Ill.
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    DNA bis-intercalation: Application of theory to the binding of echinomycin to DNA (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 431-443 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The statistical mechanical model for the binding of bifunctional intercalating ligands to duplex DNA described in the preceding paper is applied to the example of echinomycin-DNA interactions. This is the only system for which binding curves have been obtained under conditions leading to binding by both bis-intercalation and mono-intercalation simultaneously. Binding parameters and Scatchard plots are calculated for a variety of conditions. A detailed comparison of these calculations with the results from the previous analysis of the same binding data in terms of the McGhee-Von Hippel theory, assuming only one mode of binding, is presented. The results of our calculations are consistent with the model of bis-intercalation requiring the two bound chromophores of a bifunctional ligand to be separated by two base pairs. It is not necessary to assume violation of the nearest-neighbor exclusion principle, as occurred in the original analysis.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1980.360190216
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    Analysis of high-resolution melting (thermal dispersion) of DNA. Methods (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 681-700 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe the capabilities of a method for obtaining high-resolution melting profiles of short, homogeneous DNAs using a thermo-differential absorbance technique. The absorbance difference of two identical DNA solutions, raised linearly in temperature and maintained at a constant temperature difference, is monitored using a double-beam spectrophotometer. A specially constructed temperature controller and cell holder enable the temperature of the DNA samples to be controlled and monitored directly. A heating rate of 6.75°C/hr has been found to give reproducible results at ionic strengths 〉 0.01M. A method of reconstructing the true derivative from experimental data using a Taylor series expansion is described and shown to work well when the difference in temperature between samples is in the range of 0.2°C. Reconstructed derivative profiles are further analyzed by deconvolution into distinct Gaussian components. The melting profile of PM-2 DNA is shown to consist of 14 components, while the much longer lambda DNA yields 55. Related techniques such as data management and analysis for the fractional G·C content of specific domains are also described.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1980.360190316
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    Interactions of molecules with nucleic acids. VII. Intercalation and T·A specificity of daunomycin in DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 139-158 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intercalation complexes of daunomicin(+1) with tetramer duplexes in DNA are studied with the theoretically determined intercalation sites (I, -0.4), (II, -0.4), and (III, -1.4). These sites occur with base pairs separated by 6.76 Å for helical angles of 26°, 22°, and 8° about the intercalation site. Site I is preferred, and this is in agreement with experimental unwinding angles. Optimum binding positions and conformations are established, and these are in agreement with experimental results from crystal structures. A systematic procedure is devised to study base-pair and base-sequence specificity, which results in the demonstration that the most stable sequences are mainly ↑BP1, T·A, DAUN, A·T, BP4↓ and ↑BP1, T·A, DAUN, G·C, BP4↓, i.e., with the TpA and CpG (pyrimidine)p(purine) sequences about the intercalation site. These 32 possible sequences are found among the 40 most stable complexes. These theoretical calculations of intercalation complexes with daunomicin(+1) provide the first example in which a drug specifically selects the base pair T·A and prefers it in a particular sequence about the intercalation site. This specificity is in agreement with some experimental results. Problems associated with the interpretation of specificity are discussed in terms of the base, base-pair, and base-sequence resulting from the DNA site and the DNA-drug interactions. T·A specificity is rationalized by noting that the 2′deoxyribo-5′-monophosphate backbone attached to A is slightly more negative than that on the other nucleotides. Hence, a preference exists for binding to the protonated daunosamine (+1) groups. Stereographic projections of daunomycinone and daunomycin(+1) in a bond model and in a space-filling model with steric contours illustrate the results.
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    Small-angle x-ray scattering studies on yeast inorganic pyrophosphatase and its interactions with divalent metal ions, inorganic phosphate, and hydroxymethane bisphosphonate (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 159-165 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small-angle x-ray scattering studies have been carried out on the enzyme yeast inorganic pyrophosphatase (PPase), and its overall conformational changes on interaction with divalent metal ions (Mg2+ and Mn2+) and with phosphoryl ligands [inorganic phosphate (Pi) and hydroxymethane bisphosphonate (PCHOHP), a nonhydrolyzable inorganic pyrophosphate analog] were assessed. The enzyme undergoes an apparent reduction in size on simultaneous addition of Mg2+ and high Pi concentration, although neithough neither Mg2+ nor Pi added separately induced any measurable conformational changes. By contrast, simultaneous addition of Mn2+ and Pi to PPase does not result in an observable conformational change. However, the overall structure of the enzyme appears to enlarge in the simultaneous presence of Mn2+ ions and PCHOHP. The significance of the structural changes seen in PPase under various conditions is discussed.
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    Interacalation of ethidium ion into DNA and RNA oligonucleotides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 213-233 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo-oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest-neighbor exclusion. For the ribo-oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo-oligonucleotide showed all sites equivalent and no cooperativity. For the ribo-oligonucleotides the enthalpy for ethidium binding is -14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 105M-1 for the two strong sites (4 × 103M-1 for the weak site) or K = 2.5 × 105M-1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo-oligonucleotide the enthalpy of binding is -9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 104M-1).
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    Distribution of counterions around a cylindrical polyelectrolyte and manning's condensation theory (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 287-312 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of counterions around a charged polyion cylinder is calculated by several methods. First, the Debye-Hückel approximation is used, and it is shown that Manning's condensation hypothesis is necessry to avoid overneutralization of the polyion charges by the counterions when the linear-charge-density parameter, ξ, of the polyion exceeds the critical value of unity. However, it appears that this method of getting this result involves inconsistent application of Debye-Hückel theory. Therefore, we turn to the analytical solution of the Poisson-Boltzmann equation that was obtained by Alfrey, Berg, and Morawetz for a polyion cylinder plus a neutralizing number of counterions but without added salt. One of the integration constants of this solution is a radius, which we call RM, within which lies precisely the fraction of counterions that Manning assumes to condense in his theory. This radius can be rather large, however, so that the “Manning fraction” of condensed ions actually forms a diffuse cloud whose size varies with the polyelectrolyte concentration; RM varies as κ-1/2, where κ is the Debye-Hückel screening parameter. The Manning fraction, 1 - 1/ξ, and its associated radius are unique in their behavior with dilution; smaller fractions stay within finite radii, while with larger fractions the corresponding radii increase as κ-1. Thus, the condensation hypothesis does have a simple mathematical foundation in the Poisson-Boltzmann equation. Finally, by comparison with numerical solutions, we find that these conclusions are not significantly changed even when salt is added to the polyelectrolyte. A short table of numerical solutions of the Poisson-Boltzmann equation in cylindrical geometry is given, together with tables of coefficients tht enable one to discover the particular solution that applies for a given polyion radius and charge density.
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    Matrix-method calculation of linear and circular dichroism spectra of nucleic acids and polynucleotides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 435-470 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A-RNA, A-DNA, and B-DNA, when coordinates derived from x-ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum-uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long-wavelength absorption band. Using alternative conformations for DNA in low-salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B-form.In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z-DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H. & Greve, J. (1981) Biopolymers 20, 1329-1332], is in contrast with the current identification of Z-DNA with the high-salt form of poly(dGC·dGC). Finally, the optical properties of single-stranded polyribonucleotides appear to be better explained when alternative structures [91-helix for poly(rA) and 61-helix for poly(rC)] are introduced instead of the A-RNA form.
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    Total intensity light scattering from short, optically anisotropic wormlike chains (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 607-608 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230314
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    Dimensions of short, rodlike macromolecules from translational and rotational diffusion coefficients. Study of the gramicidin dimer (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 611-615 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230402
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    Alternative pathways in diffusion-collision controlled protein folding (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 675-694 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The diffusion-collision model of protein folding has been solved exactly for a three-microdomain protein subunit. Numerical analysis shows that the exact kinetics may be excellently approximated in all cases studied by a standard chemical kinetics approach with the forward rate constants calculated from the mean folding time formula found previously.
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    Electric birefringence study of the purple membrane of Halobacterium halobium (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 707-718 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An electric birefringence study was carried out on aqueous suspensions of the purple membrane of Halobacterium halobium. In addition to the characterization of both native and modified membrane samples, the dependence of electric birefringence on pH and ionic strength was also investigated. The results indicate that purple membrane shows electric birefringence at a field strength as low as 200 V/cm. The permanent dipole moment and polarizability ranged from 20,500 debyes and 1.01 × 10-14 cm3 for a purple membrane concentration of 0.40 mg/mL to 41,000 debyes and 2.05 × 10-14 cm3 for a concentration of 0.80 mg/mL. It was also found that removal of the retinyl group of bacteriorhodopsin substantially decreases but does not eliminate the electric birefringence of the membrane. The solubilization of the membrane by Triton X-100, however, completely abolishes the electric birefringence. These experiments indicate that there is an interaction between adjacent bacteriorhodopsin molecules within the purple membrane via the retinyl chromophore moiety that builds up the permanent dipole moment. They also suggest that there are two types of response when purple membrane suspensions are placed in an electric field. One is an alignment of the disk-shaped particles with the field. The other is a stacking of the particles following their alignment by the electric field, which is promoted by the induced dipole moment.
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    Folded β-turns and collagenlike conformations of -Gly-Pro- and -Pro-Gly-sequences in synthetic polytripeptides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 617-621 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Computer building of β-helical polypeptide models (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 23-38 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single- and double-stranded model helices having idealized bond lengths and angles, and any arbitrary, user-specified, pitch and number of residues per turn. The variation of inter- and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β-helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation-bound gramicidin A.
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    Conformational change in yeast tRNAAsp (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 71-81 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of yeast tRNAAsp in aqueous solutions has been analyzed in the light of results obtained from Raman spectra recorded at from 5 to 82°C and compared to those of tRNAPhe. Firm evidence is given of a reversible conformation transition for tRNAAsp at 20°C. This transition is observed for the first time in the tRNA series. The low-temperature conformation appears to have a more regular ribose-phosphate backbone and a more effective G base-stacking. This conformational change, which occurs essentially in the D loop, could be connected to the existence of two (A and B) crystal forms obtained depending on crystallization conditions. The melting temperatures, which are different for each base stacking in tRNAAsp, lie in a range of about 70°C, much higher than for tRNAPhe. This fact is interpreted by a higher ratio of G-C base pairs in tRNAAsp.
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    Interaction of poly-5-bromouridylic acid. I. Formation of helical complexes with various adenine and 2-aminoadenine derivatives (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 493-509 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9-substituted adenine and 2-aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well-resolved bands in the range of 210-350 nm. Other adenine derivative-poly(BU) complexes also afford similar CD spectra, while 2-aminoadenine derivative-poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative-poly(BU) complexes are nearly identical in structure except for the ribose-phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. The Tm of 9-methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. The Tm difference with the monomer-poly(U) system was found to be about 20°C in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0). Further, it was noted that the monomer-poly(BU) complexes are formed even when the Tm is lower than that of self-folded poly(BU).
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    31P-NMR studies of deoxyoligonucleotides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 575-592 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The assignments of 31P resonances of eight short oligonucleotides have been achieved through specific heterodecoupling techniques reported previously from our laboratory [Cheng et al. (1982) Biopolymers 21, 697-701]. The temperature dependence of the assigned 31P chemical shifts of these oligomers was studied and compared to the constitutive dimeric units. This comparison gives some insight to the chemical-shift values of the phosphorus resonances of oligonucleotides. (1) The 3′-end terminal phosphorus resonance in an oligomer tends to locate at a spectral position relatively close to its constitutive dimeric unit. (2) On chain elongation (from 5′-toward 3′-end), the phosphorus resonance in the oligomer will be shifted upfield by 0.2-0.3 ppm, as compared to its constitutive dimeric unit. (3) The relative positions of phosphorus resonances in an oligomer tend to remain in the same order as their constitutive dimeric units. The above obsrvations lead to the development of a new procedure to assign the 31P resonance of a single-stranded oligonucleotide.
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    L-Alanyl-glycylglycine: FT-IR and Raman spectroscopic evidence for tripeptide packing in a collagenlike arrangement (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 623-627 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Viscometry and sedimentation equilibrium of partially hydrolyzed hyaluronate: Comparison with theoretical models of wormlike chains (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 647-666 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fractionated samples of sodium hyaluronate of low molecular weight were used to calibrate the carbazole method for glucuronyl analsis and to determine the density increment (based on dry weight) of 0.444 (±0.003) mL/g in water and 0.386 (±0.003) mL/g for samples dialyzed against 0.2M NaCl. Weight-average molecular weights obtained by high-speed sedimentation equilibrium were used to calibrate the limiting viscosity number [η] in 0.2M NaCl, which gave [η]/Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 105. Experimental data from this work and the literature, including viscosity and light- and small-angle x-ray scattering measurements, were compared to theoretical chain models of the Kratky-Porod (KP) wormlike and the helical wormlike (HW) chain, as treated by Yamakawa and collaborators. Although either model could be fitted to experimental data about equally well with consistent parameters, provided those for the HW chain were of weakly helical nature, calculation of the unperturbed meansquare end-to-end distance as a function of chain length from a conformational model favored the KP chain alternative. The parameters that provide the best fit to experimental data for the KP wormlike model are a persistence length of 4.5-5 nm and a diameter of 1.1 nm. The latter is resonable for a hydrated hydrodynamic cylinder in view of the approximate unhydrated value of 0.7 nm estimated from the density increment.
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    Cation-induced conformational changes in tRNA molecules (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 759-766 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The uv absorption spectra and melting profiles of an initially ion-free solution of E. coli unfractionated tRNA are significantly modified by the addition of either Na+, Mg2+, or Mn2+ or of other first-series transition-metal ions such as Ni2+, Co2+, and Zn2+. The main effect of the addition of all monovalent or divalent cations examined is an increase of the ordered and stacking stabilized tRNA structure, as revealed by a drop in the absorption near 260 nm, as well as in the 4-TU absorption region. Sharp differences have, however, been detected in the 290-305-nm range in the presence of the various ions studied. When transition-metal ions were added to a tRNA solution, an absorption peak appeared at 294 nm. This effect is interpreted as a perturbation of the electronic structure of the bases due to direct binding of metal ions to the bases. An analysis of the variation in the spectrum as a function of metal concentration and of the thermal melting reversibility in the presence of various metal ions supports the conclusion that while all ions investigated are involved in binding to the phosphate groups of tRNA, transition-metal ions are also able to bind directly to the bases.
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    Electrostatic interactions between α-helix dipoles in crystals of an uncharged helical undecapeptide (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 809-817 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatic interactions between α-helix dipoles in the crystals of an uncharged helical undecapeptide have been studied in detail. The electrostatic interaction energy between one helix dipole and its 26 nearest neighbors is approximately -23 kcal mol-1. A very similar result is obtained when calculating the interactions between one helix dipole and all 988 helix dipoles occurring within a distance of 75 Å. It therefore appears that in these crystals of completely uncharged molecules large, favorable electrostatic interactions occur.
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    Modeling biological macromolecules in solution. II. The general tri-axial ellipsoid (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 843-843 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230421
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    Most-probable distribution at enzyme depolymerization of polysaccharides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 859-876 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several research groups have studied depolymerizing processes by enzyme cleavage using product distribution. Although only the shortest chain products can be measured experimentally, interpretation of much evidence requires an assumption of the nature of high polymer distribution. The present work analyzes the high polymer distribution of products on the basis of mathematical models suggested for the two most widespread α-amylase action-mechanisms. The most-probable distribution was found to be distorted by hydrolysis only for the shortest chain products. The size of the distorted region is directly dependent on the characteristics of a specific enzyme. We studied the distribution of products for substrates of varying composition to show that it approaches the most-probable distribution at depolymerization.
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    Conformation study on heparin by intermediate-angle X-ray scattering (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 995-1009 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of heparin in water was investigated by intermediate-angle x-ray scattering (IAXS). The theoretical scattering function for the coil conformation was calculated by the Monte Carlo method using the approximation of separable conformation energies and the conformation energies computed for two disaccharide pairs in heparin. From x-ray scattering in a relatively small-angle region, the conformation of heparin is not the ordered 21 helix conformation but the coil conformation obtained by the Monte Carlo calculation. It is expected, from x-ray scattering in a relatively wide-angel region, that the sulfate groups of heparin maintain about 7 Å between them.
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    Study of polysaccharides by the fluorescence method. III. Chain length dependence of the micro-Brownian motion of amylose in an aqueous solution (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1043-1056 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fluorescence polarization method was applied to the investigation of the micro-Brownian motion of amylose chains having a wide range of degree of polymerization (DP). We prepared two types of fluorescent conjugates of amylose: amylose conjugated with fluorescein randomly throughout the chain (F-amylose) and amylose conjugated locally on a terminal segment (t-F-amylose). The degree of fluorescence polarization of these conjugates was measured by changing the solvent viscosity at a constant temperature (25°C). The data obtained were analyzed by a Perrin-type equation to calculate the mean rotational relaxation time, 〈ρ〉. By examination of the plots of 〈ρ〉 vs DP, and by comparison of 〈ρ〉 with the theoretical rotational relaxation time of the whole molecule at a given DP, it was found that 〈ρ〉 mainly reflects the segmental motion of the amylose chain in the high-DP range. Thus, the fact that 〈ρ〉 for t-F-amylose is much smaller than that for F-amylose at a sufficiently high DP shows that a terminal segment undergoes a more rapid micro-Brownian motion than interior segments. In the low-DP range, we felt that the rotational diffusion of the whole molecule contributes significantly to the relaxation process. We also examined, for comparison, the segmental motion of dextran and pullulan in a similar manner and found that these segmental motions are more rapid than those of amylose. Based on the results obtained, the segmental mobility and conformation of the amylose molecule are discussed in relation to its chain length.
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    Synthesis and properties of L-cysteinyl-L-cysteine disulfides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1085-1097 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Oligomeric cyclic disulfides, obtained by mild oxidation of the fully protected dipeptide L-cysteinyl-L-cysteine, have been isolated by gel and thin-layer chromatography. Polymeric material was recycled by a thiol-disulfide exchange-reaction performed at basic pH. Spectroscopic investigations of the monomer and the two dimers indicate that conformers characterized by dihedral angles about the S—S bond close to ±90° are preferred. Moreover, chiroptical and 1H-nmr data for these compounds suggest higher mobility for the two dimers. The antiparallel dimeric disulfide can be considered a model compound for the hinge region formed at the subunit interface of the bovine seminal ribonuclease, a dimeric enzyme showing a complex kinetic behavior.
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    Dynamic light scattering as a probe of superhelical DNA-intercalating agent interaction (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1113-1119 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polarized dynamic light-scattering measurements on superhelical pBR322-plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient DT,20°C0 = (3.77 ± 0.10) × 10-8 cm2/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440-nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular-dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = -0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.
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    Quasi-harmonic method for studying very low frequency modes in proteins (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1099-1112 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quasi-harmonic approximation is described for studying very low frequency vibrations and flexible paths in proteins. The force constants of the empirical potential function are quadratic approximations to the potentials of mean force; they are evaluated from a molecular dynamics simulation of a protein based on a detailed anharmonic potential. The method is used to identify very low frequency (∼1 cm-1) normal modes for the protein pancreatic trypsin inhibitor. A simplified model for the protein is used, for which each residue is represented by a single interaction center. The quasi-harmonic force constants of the virtual internal coordinates are evaluated and the normal-mode frequencies and eigenvectors are obtained. Conformations corresponding to distortions along selected low-frequency modes are analyzed.
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    Temperature dependence of the dynamic light scattering of linear φ29 DNA: Implications for spontaneous opening of the double-helix (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1137-1137 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230613
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    Contributions of synthetic polymers of amino acids to knowledge of immune response (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1141-1141 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230615
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    Interaction of poly(I)·poly(C) with trans-dichloro-diammine-platinum (II) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1143-1143 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Analysis of the high- and low-spin soret bands of horse-heart metmyoglobin complexes (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1147-1167 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Interest in the thermodynamics of the iron-binding site in hemoproteins has increased in recent years due to refinements in x-ray crystallographic studies of hemoproteins [see Deathage, J. F., Lee, R. S., Anderson, C. M. & Moffat, K. (1976) J. Mol. Biol. 104, 687-706; Heidner, E. J., Ladner, R. C. & Perutz, M. F. (1976) J. Mol. Biol. 104, 707-722; Deathage, J. F., Lee, R. S. & Moffat, K. (1976) J. Mol. Biol. 104, 723-728; Ladner, R. C., Heidner, E. J. & Perutz, M. F. (1976) J. Mol. Biol. 114, 385-414; Fermi, G. & Perutz, M. F. (1977) J. Mol. Biol. 114, 421-431; Takano, T. (1977) J. Mol. Biol. 110, 537-568 and 569-589], the synthesis and x-ray analysis of model heme compounds [see Scheidt, W. R. (1977) Acc. Chem. Res. 10, 339-345; Kastner, M. E., Scheidt, W. R., Mashino, T. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 666-667; Mashiko, T., Kastner, M. E., Spartalian, K., Scheidt, W. R. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 6354-6362; Hill, H. A. O., Skite, P. P., Buchler, J. W., Luchr, H., Tonn, M., Gregson, A. K. & Pellizer, G. (1979) Chem. Commun. 4, 151-152; and Scheidt, W. R., Cohen, I. A. & Kastner, M. E. (1979) Biochemistry 18, 3546-3556], and the numerous data on heme-protein interactions that account for the differences observed in ligand binding between the various species of animals. Numerous probes have been used and provide information about the structure and thermodynamics of the binding site, but no single probe can provide the complete picture [see Iizuka, T. & Yonetani, T. (1970) Adv. Biophys. 1, 157-182; Smith, D. W. & Williams, R. J. P. (1970) Struct. Bond. 7, 1-45; and Spiro, T. G. (1975) Biochim. Biophys. Acta 416, 169-189].
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    Conversion from a virtual-bond chain to a complete polypeptide backbone chain (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1207-1224 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method for generating a complete polypeptide backbone structure from a set of Cα coordinates is presented. Initial trial values of φ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual-bond backbone, e.g., and α-helical region), and values of φ and ψ for the remaining residues (both towards the N- and C-terminus) are then computed, subject to the constraint that the chain have the same virtual-bond angles and virtual-bond dihedral angles as the given set of Cα coordinates. The conversion from Cα coordinates to full backbone dihedral angles (φ,ψ) involves the solution of a set of algebraic equations relating the virtual-bond angles and virtual-bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cα coordinates taken from standard-geometry full-atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error-sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cα coordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that φPro be near -75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean-square deviation of the calculated Cα coordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cα coordinates had an rms deviation of 0.26 Å from the given set of Cα coordinates was obtained.
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    Conformation of P-form DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1269-1281 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The P-Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P-form has little or no hydrogen bonding, while the data from EM show that the P-form has a condensed tertiary structure. In earlier work, we demonstrated that the P-form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P-Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P-form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non-hydrogen-bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P-form that have been observed.
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    The effects of alkali-metal chlorides and of spermidine and spermine on the swelling pressures of DNA gels in the ultracentrifuge (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1307-1313 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects is solution of the alkali-metal chlorides on the gel-like phase of DNA formed in the ultracentrifuge cell have been studied. The polycations, spermidine and spermine, also were shown to affect strongly the swelling pressure of the DNA gel, with evidence for the destabilization of DNA in very dilute spermine, below 10-6 M, and for the collapse of DNA in both spermine and spermidine solutions above 10-6 M.
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    Effect of cationic surfactants on the conformation and aggregation of poly(L-glutamic acid) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1333-1346 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of three cationic surfactants, dodecylammonium chloride (DAC), dodecyldimethylammonium chloride (DDAC), and dodecyldimethylammonium chloride (DTDAC), on the conformation of poly(L-glutamic acid) and at neutral pH were examined by CD. The maximum extent of the α-helix induction occurs for each surfactant when the mixing ration is about unity. Different effects specific to each surfactant, as described below, appear in the range of mixing ratios larger than that required for the maximum induction. In the case of DTAC, the α-helices disintegrate into random coils. In the case of DDAC, the aggregation of α-helices takes place eventually leading to precipitation. Solubilization of the precipitates occurs at high mixing ratios. The most complex behavior is seen in the case of DAC; aggregation of α-helices occurs only to a small extent and the formation of a small complex predominates over aggregation takes place again as DAC concentration increases further. Induction of the α-helix is favored by dilution at a constant mixing ratio but is suppressed by the addition of NaCl.
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    Locally oscillatory motion of RNA helix derived from linear relationships of backbone torsion angles (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1169-1184 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A linear relationship in each of the torsion angle pairs, α-β, β-∊, ∊-ζ, and α-γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers 6, 223-242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.
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    The speed of sound in DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1185-1192 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used Brillouin scattering to determine the speed of sound in (and hence longitudinal modulus of) A- and B-DNA fibers. The speed of sound is very sensitive to the degree of hydration of the fibers, and measurements have to be made at laser powers below 5 mW to avoid local heating and dehydration. Under those conditions, we obtain sound speed perpendicular to the fiber axis of about 2.2 and 1.9 km/s in A- and B-DNA fibers, respectively. A-DNA fibers show a small anisotropy with sound speeds along the fiber axis higher by up to 10% B-DNA fibers appear to be isotropic.
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    Interaction of metal ions with gastrointestinal hormones: Binding studies of Mg++ to biologically active analogs of little gastrin and minigastrin (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1225-1240 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of magnesium ions with Des-Trp1-Nle12-minigastrin I (Nle11-HG-13) and Nle115-little gastrin I (Nle15-HG-17) has been studied by CD and spectrophotometric techniques in trifluoroethanol. Spectrophotometric titrations using murexide as a metallochromic indicator showed that there are three binding sites for magnesium ions in Nle11-HG-13, with binding constants of the order of (6 ± 2) × 106, (1.7 ± 0.5) × 106, and (5.0 ± 0.5) × 105M-1. These figures have been independently confirmed by CD measurements in the far-uv in the presence of increasing amounts of magnesium ions. Elongation of the peptide chain from Nle11-HG-13 to Nle15-HG-17 does not provide any additional binding site for the metal ions. In both hormones, we have observed different responses in the near- and fur-uv CD properties with regard to added magnesium. The intensity of the CD bands in the aromatic region changes cooperatively with the ion/hormone molar ratio. These findings lead us to conclude that at the C-terminal, the biologically important sequence, -Trp-Nle-Asp-Phe-Nh2, is directly involved in the interaction with magnesium.
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    Kinetics of irreversible dissociation for proteins bound cooperatively to DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1249-1259 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one-dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of length n. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983) Biopolymers 22, 1697-1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n-2) internal positions of an n-cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero-order dissociation kinetics predicted by the Lohman model.
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    Comments on the “ordinary-extraordinary phase transition” of poly(lysine) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1637-1646 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The “ordinary-extraordinary phase transition” of poly(lysine), first reported by Lin et al. [(1978) Biopolymers 17, 1041-1064], has been reexamined as a function of the data collection interval (Δt) and scattering angle (θ). These data suggest that the relaxation domains “split” as the ionic strength is lowered through the transition region. In contrast, fluorescence photobleaching recovery data of Ware and coworkers (personal communication) indicate the tracer diffusion coefficient is not sensitive to the “ordinary-extraordinary phase transition.” The apparent discrepancy between these two techniques is here proposed to be due to small ion effects on both the dynamics and the scattering power of the polyelectrolytes.
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    Counterion binding and hydration of hyaluronate and chondroitin in solution: An 17O, 23Na, and 25Mg nuclear-magnetic-relaxation study (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1683-1699 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Nuclear magnetic relaxation rates of H217O, 23Na+, and 25Mg2+ have been measured in aqueous hyaluronate solutions. The dependence on solution pH of the relaxation rates has been investigated, as well as the competition behavior of Na+ with Ca2+ and Mg2+. H217O and 23Na+ relaxation rates in chondroitin and hyaluronate solutions have been compared in the interval, 2 ≲ pH ≲ 12.5. The ion binding of hyaluronate can be fully accounted for by Coulomb interactions, with no need to involve chemical specificity. The hydration is only slighly pH dependent, and is comparable in magnitude to hydration of synthetic polyelectrolytes and monosaccharides. Ion-binding and hydration properties of hyaluronate and chondroitin are quite similar, except at elevated pH. At alkaline pH, an increase in charge density with pH is seen in hyaluronate and, to a much lesser degree, in chondroitin, possibly due to the titration of hydroxy groups. H217O data indicate an alkali-induced transition in both glycosaminoglycans.
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    Dielectric properties of slightly hydrated collagen: Time-water content superposition analysis (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1725-1734 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The frequency dependences of the dielectric constant, ε′, and the loss factor, ε″, in collagen were measured at several water contents from 0.1 to 0.3 g/g collagen over a frequency range of 30 Hz to 100 kHz and at a temperature of 20°C. Remarkable dispersion was observed at the lower frequencies for higher water contents. According to accumulated results on the thermodynamic and structural investigations, the dispersion has some analogy to the surface conduction proposed by B. V. Hamon [(1953) Aust. J. Phys. 6, 304-315]. An empirical relation bewteen ε″ and frequency, f, ε″ ∝ fn, where 0 〈 n 〈 1, suggests that the dielectric and conductive properties of hydrated collagen are related to carrier jumps between neighboring sites. For the polarization mechanism of this dispersion, we supposed a model of the transfer of protons between absorbed water molecules, and found that the time-water content superposition procedure is applicable to slightly hydrated collagen. The results derived from the superposition procedure show that the water content, φ, is related to the conductivity, σ, or the dielectric loss factor by the following equations: σ (φ, f) = const. × φnm-1f1-n and ε″ (φ, f) = const. φnmf-n, respectively, where m is a constant independent of φ and f. These results agree with that derived by another treatment of the same data. The role of water molecules in the conduction and polarization in slightly hydrated collagen is considered to be not far from that assumed in the model.
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    Thermodynamic stability of the ordered conformations of carrageenan polyelectrolytes (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1771-1794 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Manning's counterion condensation theory has been applied to the temperature-induced conformational transition of κ- and ι-carrageenan in the solution and gel states. The formalism of the theory has been extended to transitions between conformations with charge densities below or across the counterion condensation threshold. Measurements of the dependence of the melting temperature on ionic strength, and of the enthalpy of melting, are interpreted with the theory as indicating that the conformational transition is intramolecular and that side-by-side dimerization of chains gives rise to the gel structure.
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    Azobenzene-Containing polypeptides: Photoregulation of conformation in solution (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1423-1437 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photochromic polypeptides, with 16 to 56% azobenzene groups in the side chains, have been prepared by reaction of poly(L-glutamic acid) with p-aminozaobenzene, both in the presence of dicyclohexyl carbodiimide/N-hydroxybenzotriazole and of pivaloyl chloride. Analogous modification reactions carried out on poly(L-aspartic acid) were unsuccessful owing to the formation of N-succinimide rings. In trimethylphosphate, all the azopolypeptides exhibit the α-helix CD pattern. Irradiation produces the trans-to-cis isomerization of the azo side chains, but does not induce any variations of the backbone conformation. In water, the CD spectra indicate the presence of appreciable amounts of α helix in 16 and 21% mol azo-containing poly-(Lglutamates), while a β structure is present in a 36% mol azopolypeptide. Light produces conformational changes of the polypeptide conformation which are completely reversed in the dark. The extent and kind of photobehavior depend on the azo content and the pH value at which irradiation is carried out. The light-induced effects are discussed on the basis of the pH-induced order-disorder conformational transitions. In fact, the pK values and the transition curves of the dark-adapted samples were found to be different from those of the irradiated ones.
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    Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1519-1532 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational CD (VCD) of amide I and II vibrations of several α-helical polypeptides have been measured in solution. For the amide II as well as the amide I [previously published: Lal, B.B. & Nafie, L.A. (1982) Biopolymers 21, 2161] we find the VCD to be characteristic of the polypeptide secondary structure. Amide II bands of right-handed α helices were all found to have negative VCD and to have their maximum rotational strength for the parallel (low-energy) component. However, left-handed α helices formed from L-amino acids gave positive amide II bands at higher frequencies than found for the right-handed helices, indicating that the VCD was sensitive to the stereochemical difference. The amide-I VCD spectra of some deuterated right-handed α-helical polypeptides have a new negative feature to low frequency that does not reflect theoretical predictions but also appears to be stereochemically sensitive. Amide-II and amide-A VCD of a few deuterated polypeptides imply retention of the secondary-structure-dependent characteristics seen in the hydrogenated VCD.
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    Vibrational circular dichroism of polypeptides. III. Film studies of several α-helical and β-sheet polypeptides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1533-1545 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational CD (VCD) of amides A, I, and II vibrations of a variety of polypeptide films have been measured. VCD of films of α-helical and β-sheet structures are compared in the three regions. Reproducible spectra could only be obtained for thin films free of orientation dependence. The sign and band shape of the VCD of films are not always the same as that in solution. However, the magnitude of the observed VCD seems to correlate with the secondary structure such that α-helical molecules typically have much larger Δε/ε values than do β-sheet molecules. The possibility of interference by artifacts owing to light-scattering effects is discussed.
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    Masthead (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230901
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    Structure determination of the adduct formed between the signal nucleotide diadenosine 5′, 5‴-P1, P4-tetraphosphate (Ap4A) and cis-[Pt(NH3)2Cl2] (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1623-1635 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Diadenosine 5′,5‴-P1,P4-tetraphosphate (Ap4A), an intracellular regulatory nucleotide, has been found to react with the antitumor drug cis-diamminedichloroplatinum(II) and its aqua derivative to form a single complex. This complex has been purified by high-performance liquid chromatography and characterized by 1H-nmr and CD spectroscopy. In this complex, Ap4A takes a very particular conformation. It is an N7-N7 chelate of the metal with the two adenines in a head-to-head arrangement and an anti-anti conformation of the adenosines. Platinum chelation leads to a large decrease of the Ap4A conformational flexibility.
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    Reversing-pulse electric birefringence of poly (γ-benzyl-L-glutamate). II. Field-strength dependence of steady-state and decay signals of well-fractionated samples (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1667-1681 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electric field dependence (up to 21 kV/cm) of the steady-state and decay signals has been examined on the four well-fractionated samples of poly(γ-benzyl-L-glutamate), [Glu(OBzl)]n, in N,N-dimethylformamide at 535 nm and 20°C. Together with the data previously obtained from the reversing-pulse electric birefringence [Ueda, K., Nomura, M. & Yamaoka, K. (1983) Biopolymers 22, 2077-2090], the steady-state birefringence and field-free relaxation time were analyzed by a method that takes into account the polydispersity of the chain length. The weight-average chain length, (lw), permanent dipole moment, (μw), electric polarizability anisotropy, (Δαw), and the length-independent optical anisotropy factor were evaluated. The axial translation per residue was calculated for the [Glu(OBzl)]n helix, but the uncertainly involved in the weight-average molecular weights, determined from light scattering by different investigators, makes the determination of the exact conformation of [Glu(OBzl)]n difficult. The contribution of Δαw to electric field orientation was found to be significant, since Δαw was approximately proportional to lw. A linear relationship also exists between μw and lw, when the [Glu(OBzl)]n helix is shorter than about 1200 Å.
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    Molecular theory of the helix-coil transition in polyamino acids. V. Explanation of the different conformational behavior of valine, isoleucine, and leucine in aqueous solution (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1961-1977 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Even though poly(L-valine) and poly(L-isoleucine) both contain residues that are branched at their β-carbon atoms, they exhibit a different behavior of their Zimm-Bragg helix-growth parameter s in aqueous solution. This quantity increases with temperature for poly(L-valine) but decreases for poly(L-isoleucine). The origin of this behavioral difference was examined by computing theoretical values of s versus temperature from interatomic interaction energies, taking solvent (hydrophobic and hydrophilic) effects into account. The calculated s versus temperature curves for both homopolymers are consistent with the observed experimental behavior. The two homopolymers behave differently because of differences in the change in the number of hydration-shell water molecules accompanying their helix-coil transitions. The larger isoleucine side chains are more crowded together in both the α-helical and coil forms than are those of valine. Therefore, there is a smaller change in hydration of the isoleucine side chains compared to that of the valine side chains in the helix-coil transition. By analyzing the effects of hydration on the s versus temperature curves, it is possible to account also for the experimental curve for poly(L-leucine), which exhibits an intermediate behavior between those for poly(L-valine) and poly(L-isoleucine).
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    Vibrational analysis of peptides, polypeptides, and proteins. XXIV. Conformation of poly(α-aminoisobutyric acid) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2025-2065 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman and polarized ir spectra have been obtained on built-up monomolecular films of poly(α-aminoisobutyric acid), and analyzed in the context of normal mode calculations on 310-, α-, and α′-helix conformations of this molecule. The average discrepancy between observed and calculated frequencies is significantly smaller for the 310-helix than for the other structures. This, together with the more satisfactory explanation of several special features of the spectra, indicates that this polypeptide adopts a 310-helix conformation in such thin films.
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    Resonance Raman spectra of mononucleotides obtained with 266 and 213 nm ultraviolet radiation (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2067-2081 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Resonance Raman spectra of the nucleoside 5′-monophosphates UMP, CMP, AMP, and GMP have been obtained with 266- and 213-nm radiation, the fourth and fifth harmonics of a Nd:YAG laser. The 266-nm radiation is resonant with the states giving rise to the first absorption band of the bases. The resulting spectra are in agreement with those reported previously using similar wavelength excitation but are generally of better quality. The 213-nm radiation is resonant with those states giving rise to the second strong absorption band of the bases. The spectra obtained with this wavelength show several new features relative to the 266-nm spectra, including strong enhancement of modes of the pyrimidines with a character similar to the e2g ν8 mode of benzene, relative enhancement of ring modes at 1580 and 729 cm-1 in AMP, and strong enhancement of the 1670-cm-1 C = O mode of GMP. These enhancements are discussed in terms of previously reported preresonance behavior and predicted intensities based on CNDO bond-order changes and normal-mode calculations. The results of a preliminary study of the effect of the interaction of GMP with cis-dichlorodiammineplatinum(II) on the 213-nm resonance Raman spectrum is also discussed.
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    DNA gelation in concentrated solutions (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2141-2155 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Sonicated calf-thymus DNA (200 ± 30 base pairs) spontaneously forms viscoelastic gels over a wide range of concentration, temperature, and buffer conditions. Quasielastic light scattering (QLS) can be used to monitor this process, because the ratio of dynamic-to-static scattering intensity decreases dramatically as gelation occurs. Using QLS, we have explored the effects of DNA concentration and mono- and divalent cations on the thermal stability of DNA gels. We found that the gel-sol transition temperature (Tgel) varies linearly with [DNA] from 7.5 to 17 mg/mL. Both Na+ and Mg2+ strongly stabilize the gel state. The sharpness of the transition increases with increasing ionic and DNA concentrations. Analysis of the Na+-dependent gelation indicates that the process requires the association of one Na+ per 118 base pairs. Mg2+ effectively stabilizes the gel at concentrations 10-fold below those required for Na+. The unexpectedly large effect of Mg2+ suggests that ion-specific interactions may play an important role in determining gel stability.
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    URL: http://dx.doi.org/10.1002/bip.360231104
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    Large-amplitude bending motions in phenylalanine transfer RNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2173-2193 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational energy calculations on yeast tRNAPhe reveal several likely modes of intramolecular bending, including both hingelike motions (rotations about a discrete point) and distributed flexibility (deformations that bend a double-helical segment along a smooth curve). By combining these modes of motion, the molecule can be bent from the L-shaped crystallographic structure to two extremes. It can be straightened into a nearly linear conformation at an energy cost of about 50 kcal/mol, and it can be doubled over to a conformation where the anticodon and the amino acid acceptor terminus are separated by about 40 Å at an energy cost of less than 100 kcal/mol. A bending range of over 100° can be covered for 50 kcal/mol, and we estimate that this value could be cut in half with a minimization algorithm that produced optimum stereochemistry. These energies are comparable to those that would be associated with changes in solvation due to changes in surface area as the molecule bends, indicating that there are no major steric barriers to tRNA flexibility and that variations in solvent conditions and interactions with other molecules may produce large changes in the overall conformation of tRNA.
    Additional Material: 7 Ill.
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    Premelting and the hydrogen-exchange open state in synthetic RNA duplexes (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2099-2125 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Here we attempt to relate equilibrium temperature-dependent spectral changes in two synthetic RNA homopolymer duplexes - poly(rA) · poly(rU) and poly(rI) · poly(rC) - to the conformational opening detected in stopped-flow hydrogen-deuterium exchange experiments on these molecules. We are concerned with changes in several spectral properties that occur well below onset of the thermally induced helix-coil “melting” transition in these systems. These are known as “premelting” transitions, and can be detected in uv CD spectra as well as in vibrational bands of the bases in the ir. Both CD and ir spectra exhibit isoelliptic or isosbestic points consistent with a well-defined two-state premelting process. Application of a least-squares analysis to two-state models for premelting using data from different bands in the CD and ir shows that the enthalpies are substantially greater than that of the hydrogen-exchange opening. Thus the hydrogen-exchange open state represents only one premelting reaction among several that lead to equilibrium changes in helix geometry or base vibrational modes. The latter include processes that occur on a rapid time scale, including potential base-pair openings not productive for the exchange reaction. It appears that the former, and not the hydrogen-exchange opening, dominates the premelting alterations monitored by ir and CD spectroscopy.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360231102
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    Solvation effects on the 31P-nmr chemical shifts and infrared spectra of phosphate diesters (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2157-2172 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of organic solvents on the 31P-mr chemical shifts of various phosphate diesters have been investigated in water and mixed-organic solvent systems. The addition of organic solvents to cyclic phosphates and to diethyl phosphate causes large upfield shifts of the phosphorus resonance which are attributed to solvent-induced changes in the local hydration of the phosphodiester group. This is consistent with the fact that there is an inverse correlation between the hydrogen-bond-donating ability of the solvents and the magnitude of the shifts they induce. Other possible interpretations, such as solvent-induced ion pairing and solvent-induced conformational changes, appear to be eliminated. Fourier-transform ir study of the cyclic nucletides reveals that there are also large solvent-induced shifts in the frequency of the antisymmetric OPO stretching frequency, and a comparison of the two types of measurements indicates that there is a linear correlation between shifts observed in the ir and in the 31P-nmr spectra. With UpU, the solvent-induced 31P-nmr shifts are ∼3 times smaller than those observed with the cyclic phosphates and the solvent-induced shift of the OPO band is reduced (factor of ∼1.7) as compared with the cyclic phosphates. With the single-stranded polynuclotides, poly(C) and poly(U), the solvent-induced shifts in both the nmr and ir are quite small (∼0.1 ppm and ∼1 cm-1). The very small solvent effects observed with poly(U) and poly(C) are attributed to a combination of steric effects and a polyelectrolyte effect which maintains a high density of counterions with waters of hydration in the vicinity of the charged backbone and makes the phosphates much less susceptible to solvent-induced changes in hydration.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360231105
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    Conformation of cyclic analogs of enkephalin. II. Analogs containing a cystine bridge (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2325-2334 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A systematic survey has been made, using molecular mechanics, of the conformation of the ring entity of the enkephalin analogs, [D-Cys2-L-Cys5]-enkephalinamide and [D-Cys2-D-Cys5]enkephalinamide. These molecules are considerably more flexible than the analog Tyr-cyclo(Nγ-D-A2bu-Gly-Phe-Leu-), but the favored conformations of all three are very similar. The results of these studies are compatible with a Gly3-Phe4 type II′ bend in the active conformation of enkephalin.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360231114
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    Conformational transitions and geometry differences between low-energy conformers of N-acetyl-N′-methyl alanineamide: An ab initio study at the 4-21G level with gradient relaxed geometriesPaper 34 in the series “Ab Initio Studies of Structural Features Not Easily Amenable to Experiment.” (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2335-2347 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Energy pathways between the αR, β′, C7eq, and β-regions of the conformational energy surface of N-acetyl-N′-methylalanyl amide were obtained by SCF ab initio calculations on the 4-21G level, with gradient geometry optimization at each point. The calculations indicate that no barrier exists at this computational level between αR and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail, and the most important geometrical parameters that should be treated as variables in both empirical energy calculations and in the fitting of polypeptide chains in proteins by x-ray methods are identified. In addition to the φ,ψ correlation discussed previously for the helical state, a correlation of these dihedral angles in the β-region is described.
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    URL: http://dx.doi.org/10.1002/bip.360231115
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    Calorimetric study of 2U:1A three-stranded complexes formed between poly(U) and adenine dinucleotides: ApA and diastereoisomers of nonionic adenine dideoxyribonucleoside methyl phosphonate (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2361-2382 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Melting parameters of 2U:1A complexes formed by polyuridylic acid [poly(U)] and three adenine dinucleotides, diribonucleoside monophosphonate ApA and diastereoisomers of dideoxyribonucleoside methyl phosphonate [(dApA)1 and (dApA)2], in 1M NaCl and at a number of dinucleotide concentrations were obtained from differential scanning microcalorimetric data and interpreted in terms of the theory of helix-coil equilibrium in oligonucleotide-polynucleotide systems. The apparent binding constant, 1/cm, at 39°C and melting temperatures, Tm, at 1 × 10-3 M dinucleotide concentration indicate the following order of thermodynamic stability of the complexes: 2 poly(U) · (dApA)2 (2.27 × 103M-1, 44.2°C) 〉 2 poly(U) · (dApA)1 (9.9 × 102M1, 39.2°C) 〉 2 poly(U) · (ApA) (5.9 × 102M-1, 35.8°C). Corresponding calorimetric enthalpies of melting, ΔHm: 13.5, 12.7, and 12.8 kcal/mol (UUA base triplets) were found to be considerably lower than the van't Hoff enthalpies, ΔHapp: 29.4, 16.2, and 16.2 kcal/mol, respectively, evaluated from the dependence of the melting temperatures on dinucleotide concentration. Self-association of dinucleotides and their simultaneous binding as monomers, dimers, and higher-order associated species is suggested as the most probable cause of the differences between ΔHm and ΔHapp values. The differences in thermodynamic properties of the complexes formed by (dApA)1 and (dApA)2 diastereoisomers are discussed in connection with their known conformational properties. The higher and essentially enthalpic stability of the 2 poly(U) · (dApA)2 complex correlates with a lower degree of intramolecular stacking of the (dApA)2 isomer. The hydrophobically enhanced strong self-association of the latter greatly influences the thermodynamics of its complex formation with poly(U) and results in ΔHapp/ΔHm = 2.3.
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    Differential electrostatic stabilization of A-, B-, and Z-forms of DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2743-2759 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The static accessibility discrete charge algorithm for protein charge interactions is extended to the case of linear polyelectrolytes. In this model, the effective dielectric value between surface charge sites depends predominantly on the solvent ionic strength and the solvent accessibilities of the charge sites. This treatment accounts for the phenomena of specific ion binding in the context of a general electrostatic effect [Matthew and Richards (1982) Biochemistry 21, 4989]. Specific ion sites are determined by locating areas of high electrostatic potential at the solvent interface of the macromolecule. At a given ionic strength the calculated potential at a site is taken to describe a binding constant and therefore the ion site occupancy. For a 20-base-pair fragment of B-DNA, net charge of -40, 16 ion sites are indicated in the minor groove. The partial occupancy of each site increases from 0.2 to 0.5 as the ionic strength is increased from 0.01 to 0.50. Over the same range of ionic strength, the electrostatic free energy of this charge array is calculated to change from +0.6 to -0.05 kcal/bp. Parallel behavior is predicted for A- and Z-DNA charge geometries. The most stable configuration, based on electrostatic criteria, at high ionic strength (I = 0.1-0.5) is that of Z-DNA. In this range, the ratio of “bound” sodium to phosphate is predicted to be less than 0.4.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360231205
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    Role of proline … proline interactions in the packing of collagenlike poly(tripeptide) triple helices (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2781-2799 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational energy computations were carried out on the packing of two identical collagenlike poly(tripeptide) triple helices in order to determine the energetics of favorable packing arrangements as a function of composition and chain length. The triple helices considered were [CH3CO-(Gly-Pro-Pro)nt-NHCH3]3 and [CH3CO-(Gly-Pro-Ala)nt-NHCH3]3, with nt = 3, 4, and 5. The packing arrangements were characterized in terms of their intermolecular energies and orientation angles Ω0 of the axes of the two triple helices. For short triple helices (nt = 3 or 4), many low-energy orientations, with a wide range of values of Ω0, can occur. When the triple helices are longer (nt = 5), the only low-energy packing arrangements of two poly(Gly-Pro-Pro) triple helices are those with a nearly parallel orientation of the two helix axes, with Ω0 ≈ -10°. This result accounts for the observed parallel (rather than antiparallel) arrangement of collagen molecules in microfibril assembly and stands in contrast to the preferred antiparallel arrangement of a pair of α-helices. Since the preference for a parallel arrangement of these collagenlike triple helices is less pronounced in the case of poly(Gly-Pro-Ala), it appears that this preference is a consequence of the frequent presence of imino acids in position Y of the Gly-X-Y repeating triplet. In poly(Gly-Pro-Ala), most of the low-energy packing arrangements are parallel, but a few arrangements with low energies and high values of |Ω0| occur. These packing arrangements have a high energy, however, when Pro is substituted for Ala, and thus they are not accessible for collagen with natural amino (imino) acid sequences. The computations reported here account for some of the characteristic features of collagen packing in terms of the local interaction energies of a pair of triple helices.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360231207
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    Low-frequency dynamics of solid poly(L-alanine) from Raman spectroscopy (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 2891-2899 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman modes from amorphous α-helical poly(L-alanine) in the low-frequency region 〈 150 cm-1 have been observed and assignments and values compared with mode-analysis calculations. The temperature dependence of the complete Raman spectrum of α-poly(L-Ala) is also reported.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360231213
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    A monte-carlo estimate of DNA loop formation (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 601-605 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ends of rather short double-helical DNA segments (approximately two persistence lengths) can be enzymatically joined to form closed circles. Such covalent closure into circles is a measure of the likelihood of the two ends of the DNA coming into close contact. There is a length of DNA for which loop formation is most likely to occur. We have determined the chain-length dependence of loop formation for stiff chains using computer-generated chains of cylinders. The distribution from which the values for the angles between cylinders were chosen relates the chain parameters to a given chain persistence. Our results are compared with those of other theories, including a statistical wormlike chain model, and with the experimental measurements for ring closure of DNA restriction fragments.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230313
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    Masthead (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360230401
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    Intercalation of cationic dyes in the DNA double helix: Introductory theory (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 629-645 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of salt on the intercalation of acridine dyes and DNA is rather well explained by the Gouy-Chapman double-layer theory as applied to a cylinder model of the DNA-dye complex. The free energy of transfer of a dye ion from the bulk solution to the complex is divided into several parts, one of which, ΔF0, accounts for the short-range, nonelectrostatic interactions. The assumption that ΔF0 should not depend on the amount of dye in the complex leads to an internal dielectric constant of the cylinder of about Di = 7. The scatter in ΔF0 values, as calculated from individual experimental points, is of order 0.5 kT per dye ion. This scatter is large enough to mask possible effects of heterogeneity in DNA sequences. The calculations are made for a long cylinder with radius 10 Å, with the DNA phosphate charges smeared uniformly at the surface, a uniform spacing of dye charges at the cylinder axis, and a length of b = 3.37 Å per base pair. Each intercalated dye ion also adds a length b to the total length of the cylinder. The salt-dependent part of the electric free energy of intercalation, ΔF1, is tabulated for complexes with r = 0-0.24 dye ions per DNA phosphate in 0.002-0.2M monovalent salt and dye solutions.
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    URL: http://dx.doi.org/10.1002/bip.360230405
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    Proton polarizability of poly(L-tyrosine)-hydrogen phosphate hydrogen bonds as a function of alkali cations (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 695-705 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied films of poly(L-tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li+, Na+, K+) and of the degree of hydration were clarified. If Li+ ions are present, the OH⃛-OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate-hydrogen phosphate hydrogen bonds is prevented by the presence of the Li+ ions. With an increase in the degree of hydration, the tyrosine-phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K+ ions are present. In dry films, the OH⃛-OP ⇌ O-⃛HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K+ ions when compared to the system with Li+ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K+ ions. Furthermore, POH⃛-OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine-hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the -PO3- groupings are in a symmetrical environment, indicating that the K+ ions are removed from these groupings. If the degree of hydration increases further, hydrogen-bonded systems such as hydrogen phosphate-water-hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na+ ions are present, the OH⃛-OP ⇌ O-⃛HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.
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    URL: http://dx.doi.org/10.1002/bip.360230409
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    Mechanism of gel formation in κ-carrageenan (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 735-745 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a general view of κ-carrageenan gelation and some new experimental results concerning their behavior in the presence of Na+, K+, or Rb+ counterions in semidilute concentration. The gelation mechanism is based on the aggregation of helical dimers.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230412
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    Neue Wege zu 1H- und 2H-Pyrrolen (1980)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 63 (1980), S. 658-663 
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    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: New Routes to 1H- and 2H-PyrrolesA synthesis of 1H-pyrroles is described starting with pyridine analogues of chalcones and involving the reaction of acetic anhydride with 1-pyrroline-1-oxides. Another route leads from 1-pyrrolines to 2 H-pyrroles via bromination with N-bromosuccinimide and subsequent dehydrobromination in dimethylformamide.
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    URL: http://dx.doi.org/10.1002/hlca.19800630313
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    Erratum (1980)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 63 (1980), S. 681-681 
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    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19800630317
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    Nucleophilic addition to C,C double bonds. IIIFor Part I, see [1]; for Part II, see [2].. Chemical reactivity of 1endo, 4endo: 5exo, 8exo-dimethano-1,2,3,4,4a,5,8,8a-octahydronaphthalen-10syn-ol and X-ray structure analysis of its p-nitrobenzoate (1980)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 63 (1980), S. 674-681 
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    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The title compound 1 is a further example of an olefinic alcohol that undergoes ether formation under basic conditions (→ 3) although the double bond is not activated by an electron-attracting group. This unusual reactivity is due to steric compression, which is increased in the 10-methyl analogue 2. This forms the corresponding ether 7 at a much higher rate. - In a deuteriated medium, base-catalysed cyclization of 1 gives the exo-deuteriated ether 6, corresponding to trans-addition. - An X-ray structure analysis of 4, the p-nitrobenzoate of 1, is presented.
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    URL: http://dx.doi.org/10.1002/hlca.19800630316
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